Related papers: A proposal to a generalised splicing with a self a…
Splicing systems are generative mechanisms introduced by Tom Head in 1987 to model the biological process of DNA recombination. The computational engine of a splicing system is the "splicing operation", a cut-and-paste binary string…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…
The string splicing was introduced by Tom Head which stands as an abstract model for the DNA recombination under the influence of restriction enzymes. The complex chemical process of three dimensional molecules in three dimensional space…
This paper outlines an application of iterated version of generalised sequential crossover of two languages (which in some sense, an abstraction of the crossover of chromosomes in living organisms) in studying some classes of the newly…
Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly thereafter, it was proven that the languages…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
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…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Compositional generalization is one of the main properties which differentiates lexical learning in humans from state-of-art neural networks. We propose a general framework for building models that can generalize compositionally using the…
Amidst all candidates of physics beyond the Standard Model, string theory provides a unique proposal for incorporating gauge and gravitational interactions. In string theory, a four-dimensional theory that unifies quantum mechanics and…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
In this paper we present a model containing modifications to the Signal-passing Tile Assembly Model (STAM), a tile-based self-assembly model whose tiles are capable of activating and deactivating glues based on the binding of other glues.…
Composite function minimization captures a wide spectrum of applications in both computer vision and machine learning. It includes bound constrained optimization, $\ell_1$ norm regularized optimization, and $\ell_0$ norm regularized…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
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…
We calculate the partition function of the $SU(N)$ ( and $U(N)$) generalized $YM_2$ theory defined on an arbitrary Riemann surface. The result which is expressed as a sum over irreducible representations generalizes the Rusakov formula for…