Related papers: Autonomous push-down automaton built on DNA
This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…
Three reasonable hypotheses lead to the thesis that physical phenomena can be described and simulated with cellular automata. In this work, we attempt to describe the motion of a particle upon which a constant force is applied, with a…
DNA-based nanonetworks have a wide range of promising use cases, especially in the field of medicine. With a large set of agents, a partially observable stochastic environment, and noisy observations, such nanoscale systems can be modelled…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
The linear-time simulation of 2-way deterministic pushdown automata (2DPDA) by the Cook and Jones constructions is revisited. Following the semantics-based approach by Jones, an interpreter is given which, when extended with random-access…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
The theory of computation is based on abstract computing automata which can be classified into a three-class hierarchy: Finite Automata (FA), Push-down Automata (PDA) and the Turing Machines (TM). Each class corresponds to grammar/language…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
A cellular automaton that is a generalization of the box-ball system with either many kinds of balls or finite carrier capacity is proposed and studied through two discrete integrable systems: nonautonomous discrete KP lattice and…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Deep Neural Networks (DNNs) are built using artificial neural networks. They are part of machine learning methods that are capable of learning from data that have been used in a wide range of applications. DNNs are mainly handcrafted and…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
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…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
Dynamical systems are capable of performing computation in a reservoir computing paradigm. This paper presents a general representation of these systems as an artificial neural network (ANN). Initially, we implement the simplest dynamical…
Cellular automata have long been celebrated for their ability to generate complex behaviors from simple, local rules, with well-known discrete models like Conway's Game of Life proven capable of universal computation. Recent advancements…
Machine learning, particularly in the form of deep learning, has driven most of the recent fundamental developments in artificial intelligence. Deep learning is based on computational models that are, to a certain extent, bio-inspired, as…
We have micromachined a silicon-chip device that transports DNA with a Brownian ratchet that rectifies the Brownian motion of microscopic particles. Transport properties for a DNA 50mer agree with theoretical predictions, and the DNA…
Branched junction molecule assembly of DNA nanostructures, pioneered by Seeman's laboratory in the 1980s, has become increasingly sophisticated, as have the assembly targets. A critical design step is finding minimal sets of branched…
Bottom-up fabrication of inorganic nanostructures is emerging as an alternative to classical top-down approaches, offering precise nanometer-scale control at relatively low cost and effort. In particular, DNA nanostructures provide…