Soliton-like Solution on the Dynamics of Modified Peyrard-Bishop DNA Model in the Thermostat as a Bio-Fluid

Abstract

The Peyrard-Bishop (PB) DNA model is the most representative model to investigate DNA dynamics because the model is able to answer DNA denaturation processes even though the model has restricted review that DNA assumes without surrounding interaction. In this study, we investigate the dynamics of the modified PB DNA model by considering DNA in the Nosé-Hoover thermostat as a bio-fluid with various viscosities. Viscosity variations are reviewed through temperature variations, namely thermal viscosity. We attain the dynamical equation of DNA in the form of a nonlinear Schrödinger-like (NLS-like) equation by using the perturbation method and continuous approximation. We solve the NLS-like equations by the numerical split-step Fourier method. We obtain a soliton-like solution for the dynamics of this specific DNA model. The behavior of the soliton-like solution fluctuates as the temperature increases, representing the fluctuational openings of DNA, i.e., denaturation bubbles. In addition, that behavior also evolves with variations of the perturbation parameter. Moreover, we obtain soliton-like solutions by balancing the perturbation and the nonlinearity of the DNA system from the bio-fluid interaction. Furthermore, for the specific thermal viscosity of bio-fluid, we gain the denaturation temperature at 370 K ≤ T ≤ 380 K. Doi: 10.28991/ESJ-2022-06-04-01 Full Text: PDF

A Comparative Study of Hybrid Analytical and Laplace Transform Approaches for Solving Partial Differential Equations in Python

“…Their findings contribute to a deeper understanding of the complex behavior of proteins. In the study conducted by Sutantyo et al (37), they have investigated the impact of heat exchanger design on heat transfer rate and temperature distribution. They analyzed different heat exchanger designs and evaluate their heat transfer efficiency and temperature distribution performance.…”

Characterize Type of Splicing Languages via Directed Splicing Graph

“…The genetic makeup of an organism is made up of DNA which consists of nucleotides [4]. Each molecule of the DNA subunit is made up of three parts; nitrogenous bases, deoxyribose sugar, and a phosphate group.…”

Spline-in-compression approximation of order of accuracy three (four) for second order non-linear IVPs on a graded mesh

“…Sutantyo et al. [ 20 ] developed a soliton-like solution on the dynamics of the transformed Peyrard-Bishop DNA model in the thermostat as a bio-fluid. It has been experienced in the past that the high accuracy numerical solution of IVPs fails to compute the solution near the vicinity of the singular point at t=0 [ 4 , 6 , 15 , 17 ].…”