Related papers: Autonomous push-down automaton built on DNA
Several kinds of quantum pushdown automaton models have been proposed, and their computational power is investigated intensively. However, for some quantum pushdown automaton models, it is not known whether quantum models are at least as…
With conventional silicon-based computing approaching its physical and efficiency limits, biocomputing emerges as a promising alternative. This approach utilises biomaterials such as DNA and neurons as an interesting alternative to data…
Recent advancements in microbiology have motivated the study of the production of nanostructures with applications such as biomedical computing and molecular robotics. One way to construct these structures is to construct branched DNA…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
In recent years, the modeling interest has increased significantly from the molecular level to the atomic and quantum scale. The field of computational chemistry plays a significant role in designing computational models for the operation…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
In a probabilistic cellular automaton in which all local transitions have positive probability, the problem of keeping a bit of information indefinitely is nontrivial, even in an infinite automaton. Still, there is a solution in 2…
We study decidability of verification problems for timed automata extended with unbounded discrete data structures. More detailed, we extend timed automata with a pushdown stack. In this way, we obtain a strong model that may for instance…
Deoxyribonucleic acid is increasingly being understood to be an informational molecule, capable of information processing.It has found application in the determination of non-deterministic algorithms and in the design of molecular computing…
Any algorithm (in the sense of Gurevich's abstract-state-machine axiomatization of classical algorithms) operating over any arbitrary unordered domain can be simulated by a dynamic cellular automaton, that is, by a pattern-directed cellular…
In this paper, we give a deterministic pushdown transducer and a normal sequence of digits compressed by it. This solves positively a question left open in a previous paper by V. Becher, P. A. Heiber and the first author.
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
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…
In the last two decades, DNA self-assembly has grown into a major area of research attracting people from diverse background. It has numerous potential applications such as targeted drug delivery, artificial photosynthesis etc. In the last…
This position paper presents a vision for self-driving particle accelerators that operate autonomously with minimal human intervention. We propose that future facilities be designed through artificial intelligence (AI) co-design, where AI…
Weighted pushdown automata (WPDAs) are at the core of many natural language processing tasks, like syntax-based statistical machine translation and transition-based dependency parsing. As most existing dynamic programming algorithms are…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
Flow-driven rotary motors drive functional processes in human society such as windmills and water wheels. Although examples of such rotary motors also feature prominently in cell biology, their synthetic construction at the nanoscale has…