IDEAS home Printed from https://ideas.repec.org/a/gam/jmathe/v12y2024i14p2275-d1439550.html
   My bibliography  Save this article

Numerical Investigation of Nucleotides’ Interaction Considering Changes Caused by Liquid Influences

Author

Listed:
  • Raimondas Jasevičius

    (Institute of Mechanical Science, Faculty of Mechanics, Vilnius Gediminas Technical University, Plytinės Str. 25, 10105 Vilnius, Lithuania)

Abstract

This work is devoted to the interaction of nucleotides. The goal of this study is to learn or try to learn how the interaction between nucleotides with exposure to a liquid takes place. Will the interacting forces of the nucleotides be sufficient to approach the incision? A numerical imitation of the interaction is conducted using the discrete element method and a Gears predictor–corrector as part of the integrated scheme. In this work, the results reflect the dynamics of nucleotides: velocity, displacement, and force graphs are presented with and without the effect of the liquid. During changes caused by the influence of a liquid, the nucleotide interaction transforms and passes three stages: a full stop, one similar to viscous damping, and one similar to non-dissipative behaviors. The main contribution of this work is a better understanding of the behavior of infinitely small objects that would be difficult to observe in vivo. The changing influence of a liquid can transform into certain effects. As a result, a model is provided, which can be based on the results of well-known physical experiments (DNA unzipping) for modeling nucleotide interactions.

Suggested Citation

  • Raimondas Jasevičius, 2024. "Numerical Investigation of Nucleotides’ Interaction Considering Changes Caused by Liquid Influences," Mathematics, MDPI, vol. 12(14), pages 1-17, July.
    • Handle: RePEc:gam:jmathe:v:12:y:2024:i:14:p:2275-:d:1439550
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2227-7390/12/14/2275/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2227-7390/12/14/2275/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. Chi, Qingjia & Wang, Guixue & Jiang, Jiahuan, 2013. "The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 392(5), pages 1072-1079.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Lidice González & Daniel Kolbin & Christian Trahan & Célia Jeronimo & François Robert & Marlene Oeffinger & Kerry Bloom & Stephen W. Michnick, 2023. "Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Deepak Karna & Eriko Mano & Jiahao Ji & Ibuki Kawamata & Yuki Suzuki & Hanbin Mao, 2023. "Chemo-mechanical forces modulate the topology dynamics of mesoscale DNA assemblies," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Nathalie Casanova-Morales & Nataniel L Figueroa & Karol Alfaro & Felipe Montenegro & Nelson P Barrera & J R Maze & Christian A M Wilson & Pablo Conejeros, 2019. "Structural characterization of the saxitoxin-targeting APTSTX1 aptamer using optical tweezers and molecular dynamics simulations," PLOS ONE, Public Library of Science, vol. 14(11), pages 1-14, November.
    4. Jiaqi Yan & Rajendra Bhadane & Meixin Ran & Xiaodong Ma & Yuanqiang Li & Dongdong Zheng & Outi M. H. Salo-Ahen & Hongbo Zhang, 2024. "Development of Aptamer-DNAzyme based metal-nucleic acid frameworks for gastric cancer therapy," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jmathe:v:12:y:2024:i:14:p:2275-:d:1439550. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.