The traveling car renter problem (TCRP) is a variant of the Traveling Salesman Problem (TSP) wherein the salesman utilizes rented cars for travel. The primary objective of this problem is to identify a solution that minimizes the cumulative operating costs. Given its classification as a non-deterministic polynomial (NP) problem, traditional computers are not proficient in effectively resolving it. Conversely, DNA computing exhibits unparalleled advantages when confronted with NP-hard problems. This paper presents a DNA algorithm, based on the Adleman-Lipton model, as a proposed approach to address TCRP. The solution for TCRP can be acquired by following a series of fundamental steps, including coding, interaction, and extraction. The time computing complexity of the proposed DNA algorithm is O(nm) for TCRP with n cities and m types of cars. By conducting simulation experiments, the solutions for certain instances of TCRP are computed and compared to those obtained by alternative algorithms. The proposed algorithm further illustrates the potential of DNA computing, as a form of parallel computing, to address more intricate large-scale problems.
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http://dx.doi.org/10.1109/TNB.2024.3396142 | DOI Listing |
Calcif Tissue Int
January 2025
Department of Pharmacology, Tokyo Dental College, 2-9-18, Kandamisaki-cho, Chiyoda-ku, Tokyo, 101-0061, Japan.
Hypophosphatasia (HPP) is a congenital bone disease caused by tissue-nonspecific mutations in the alkaline phosphatase gene. It is classified into six types: severe perinatal, benign prenatal, infantile, pediatric, adult, and odonto. HPP with femoral hypoplasia on fetal ultrasonography, seizures, or early loss of primary teeth can be easily diagnosed.
View Article and Find Full Text PDFGenome Biol
January 2025
Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
We investigate alternative strategies against reference bias and postmortem damage in low coverage paleogenomes. Compared to alignment to the linear reference genome, we show that masking known polymorphic sites and graph alignment effectively remove reference bias, but only starting from raw read files. We next study approaches to overcome postmortem damage: trimming, rescaling, and our newly developed algorithm, bamRefine (github.
View Article and Find Full Text PDFPLoS Comput Biol
January 2025
Department of Gastroenterology and Hepatology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
Quantification of intrahepatic covalently closed circular DNA (cccDNA) is a key for evaluating an elimination of hepatitis B virus (HBV) in infected patients. However, quantifying cccDNA requires invasive methods such as a liver biopsy, which makes it impractical to access the dynamics of cccDNA in patients. Although HBV RNA and HBV core-related antigens (HBcrAg) have been proposed as surrogate markers for evaluating cccDNA activity, they do not necessarily estimate the amount of cccDNA.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Biology, Georgetown University, Washington, DC, United States of America.
Genomics is an increasingly important part of biology research. However, educating undergraduates in genomics is not yet a standard part of life sciences curricula. We believe this is, in part, due to a lack of standard concepts for the teaching of genomics.
View Article and Find Full Text PDFBioinformatics
January 2025
Institute for Computational Systems Biology, Universität Hamburg, Hamburg, 22761, Germany.
Motivation: Transcription factors (TFs) are DNA-binding proteins that regulate gene expression. Traditional methods predict a protein as a TF if the protein contains any DNA-binding domains (DBDs) of known TFs. However, this approach fails to identify a novel TF that does not contain any known DBDs.
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