Related papers: On Algebraic Approaches for DNA Codes with Multipl…
Designing channel codes under low-latency constraints is one of the most demanding requirements in 5G standards. However, a sharp characterization of the performance of traditional codes is available only in the large block-length limit.…
This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
Context: Detecting arrays are mathematical structures aimed at fault identification in combinatorial interaction testing. However, they cannot be directly applied to systems that have constraints among test parameters. Such constraints are…
We propose a new construction for low-density source codes with multiple parameters that can be tuned to optimize the performance of the code. In addition, we introduce a set of analysis techniques for deriving upper bounds for the expected…
The study of Armstrong codes is motivated by the problem of understanding complexities of dependencies in relational database systems, where attributes have bounded domains. A $(q,k,n)$-Armstrong code is a $q$-ary code of length $n$ with…
The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6…
In real-world, many problems can be formulated as the alignment between two geometric patterns. Previously, a great amount of research focus on the alignment of 2D or 3D patterns, especially in the field of computer vision. Recently, the…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Optimal recursive decomposition (or DR-planning) is crucial for analyzing, designing, solving or finding realizations of geometric constraint sytems. While the optimal DR-planning problem is NP-hard even for general 2D bar-joint constraint…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
This article is devoted to applications of projection operators to simulate phenomenological properties of the molecular-genetic code system. Oblique projection operators are under consideration, which are connected with matrix…
Given a set of sequences, the distance between pairs of them helps us to find their similarity and derive structural relationship amongst them. For genomic sequences such measures make it possible to construct the evolution tree of…
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…
The early promises of DNA computing to deliver a massively parallel architecture well-suited to computationally hard problems have so far been largely unkept. Indeed, it is probably fair to say that only toy problems have been addressed…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Let $A(n, d)$ denote the maximum size of a binary code of length $n$ and minimum Hamming distance $d$. Studying $A(n, d)$, including efforts to determine it as well to derive bounds on $A(n, d)$ for large $n$'s, is one of the most…