Related papers: Simulating 3-symbol Turing machines with SIMD||DNA
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an…
In the current world due to the huge demand for storage, DNA-based storage solution sounds quite promising because of their longevity, low power consumption, and high capacity. However in real life storing data in the form of DNA is quite…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
DNA self-assembly is a robust and programmable approach for building structures at nanoscale. Researchers around the world have proposed and implemented different techniques to build two dimensional and three dimensional nano structures.…
Labelling data is expensive and time consuming especially for domains such as medical imaging that contain volumetric imaging data and require expert knowledge. Exploiting a larger pool of labeled data available across multiple centers,…
Neural networks powered with external memory simulate computer behaviors. These models, which use the memory to store data for a neural controller, can learn algorithms and other complex tasks. In this paper, we introduce a new memory to…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Nanopore sequencing offers the ability for real-time analysis of long DNA sequences at a low cost, enabling new applications such as early detection of cancer. Due to the complex nature of nanopore measurements and the high cost of…
With the progressive scale-down of semiconductor's feature size, people are looking forward to More Moore and More than Moore. In order to offer a possible alternative implementation process, people are trying to figure out a feasible…
Neural networks possess incredible capabilities for extracting abstract features from data. Electromagnetic computing harnesses wave propagation to execute computational operations. Metasurfaces, composed of subwavelength meta-atoms, are…
Large language models (LLMs) have transformed artificial intelligence, but their computational requirements remain prohibitive for most users. Standard inference demands expensive datacenter GPUs or cloud API access, leaving over one…
We introduce a new type of generalized Turing machines (GTMs), which are intended as a tool for the mathematician who studies computability in Analysis. In a single tape cell a GTM can store a symbol, a real number, a continuous real…
DNA computing is an unconventional approach to computing that harnesses the parallelism and information storage capabilities of DNA molecules. It has emerged as a promising field with potential applications in solving a variety of…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
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…
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…
Non-volatile Memory (NVM) technologies present a promising alternative to traditional volatile memories such as SRAM and DRAM. Due to the limited availability of real NVM devices, simulators play a crucial role in architectural exploration…
Tensor permutation is a fundamental operation widely applied in AI, tensor networks, and related fields. However, it is extremely complex, and different shapes and permutation maps can make a huge difference. SIMD permutation began to be…
DNA computing, a nontraditional computing mechanism, provides a feasible and effective method for solving NP-hard problems because of the vast parallelism and high-density storage of DNA molecules. Although DNA computing has been exploited…
Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…