Showing papers on "Molecular models of DNA published in 2020"
TL;DR: In this paper, the Peyrard-Bishop DNA dynamic model equation is studied analytically by hyperbolic and exponential ansatz methods and numerically by finite difference method.
Abstract: In this work, we introduce a numerical and analytical study of the Peyrard-Bishop DNA dynamic model equation. This model is studied analytically by hyperbolic and exponential ansatz methods and numerically by finite difference method. A comparison between the results obtained by the analytical methods and the numerical method is investigated. Furthermore, some figures are introduced to show how accurate the solutions will be obtained from the analytical and numerical methods.
103 citations
TL;DR: By the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely.
Abstract: The DNA molecule is the most evolved and most complex molecule created by nature. The primary role of DNA in medicine is long-term storage of genetic information. Genetic modifying is one of the most critical challenges that scientists face. On the other hand, it is said that under the influence of acoustic, electromagnetic, and scalar waves, the genetic code of DNA can be read or rewritten. In this article, the most accurate and comprehensive dynamic model will be presented for DNA. Each of the two strands is modeled with an out of plane curved beam and then by doubling this two strands with springs, consider the hydrogen bond strength between this two strands. Beams are traditionally descriptions of mechanical engineering structural elements or building. However, any structure such as automotive automobile frames, aircraft components, machine frames, and other mechanical or structural systems contain beam structures that are designed to carry lateral loads are analyzed similarly. Also, in this model, the mass of the nucleobases in the DNA structure, the effects of the fluid surrounding the DNA (nucleoplasm) and the effects of temperature changes are also considered. Finally, by deriving governing equations from Hamilton's principle method and solving these equations with the generalized differential quadrature method (GDQM), the frequency and mode shape of the DNA is obtained for the first time. In the end, validation of the obtained results from solving the governing equations of mathematical model compared to the obtained results from the COMSOL software is confirmed. By the help of these results, a conceptual idea for controlling cancer with using the DNA resonance frequency is presented. This idea will be presented to stop the cancerous cell's protein synthesis and modifying DNA sequence and genetic manipulation of the cell. On the other hand, by the presented DNA model and by obtaining DNA frequency, experimental studies of the effects of waves on DNA such as phantom effect or DNA teleportation can also be studied scientifically and precisely.
11 citations
TL;DR: A model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally is arrived at.
Abstract: About three-quarters of eukaryotic DNA is wrapped into nucleosomes; DNA spools with a protein core. The affinity of a given DNA stretch to be incorporated into a nucleosome is known to depend on the base-pair sequence-dependent geometry and elasticity of the DNA double helix. This causes the rotational and translational positioning of nucleosomes. In this study we ask the question whether the latter can be predicted by a simple coarse-grained DNA model with sequence-dependent elasticity, the rigid base-pair model. Whereas this model is known to be rather robust in predicting rotational nucleosome positioning, we show that the translational positioning is a rather subtle effect that is dominated by the guanine-cytosine content dependence of entropy rather than energy. A correct qualitative prediction within the rigid base-pair framework can only be achieved by assuming that DNA elasticity effectively changes on complexation into the nucleosome complex. With that extra assumption we arrive at a model which gives an excellent quantitative agreement to experimental in vitro nucleosome maps, under the additional assumption that nucleosomes equilibrate their positions only locally.
8 citations
TL;DR: In this paper, the Peyrard-Bishop DNA model is replaced with a non-linear 1D Hamiltonian with a twist angle dependence, which is based on a Hamiltonian that does not consider the helical twist or any other relevant molecular dimensions.
7 citations
TL;DR: All the physics models, DNA models, and direct damage thresholds investigated in this study are applicable to predict energy deposition and DNA damage although the choice of parameters can lead to disparity in simulation results, which serves as a reference for future studies.
Abstract: Purpose Monte Carlo (MC) track structure codes are commonly used for predicting energy deposition and radiation-induced DNA damage at the nanometer scale. Various simulation parameters such as physics model, DNA model, and direct damage threshold have been developed. The differences in adopted parameters lead to disparity in calculation results, which requires quantitative evaluation. Methods Three simulation configurations were implemented in TOPAS-nBio MC toolkit to investigate the impact of physics models, DNA model, and direct damage threshold on the prediction of energy deposition and DNA damage. Dose point kernels (DPKs) of electrons and nanometer-sized volumes irradiated with electrons, protons, and alpha particles were utilized to evaluate the impact of physics models on energy deposition. Proton irradiation of plasmid DNA was used to investigate the disparity in single-strand break and double-strand break (DSB) yields caused by differences in physics models, DNA models, and direct damage thresholds. Results Electron DPKs obtained with different physics models show similar trends but different diffusiveness and maximums. Energy deposition distributions in nanometer-sized volumes irradiated with electrons, protons, and alpha particles calculated using different physics models have the same trend although discrepancies can be observed at the lowest and highest energy deposits. Strand breaks from incident protons in DNA plasmids vary with adopted parameters. For the configurations in this study, changing physics model, DNA model, and direct damage threshold can cause differences of up to 57%, 69%, and 15% in DSB yields, respectively. All these simulation results are essentially in agreement with previously published simulation or experimental studies. Conclusion All the physics models, DNA models, and direct damage thresholds investigated in this study are applicable to predict energy deposition and DNA damage. Although the choice of parameters can lead to disparity in simulation results, which serves as a reference for future studies.
7 citations
TL;DR: In this article, Monte Carlo simulations were used to classify DNA damage into different types and predict the amount of energy deposited, and Geant4-DNA was used to predict simple and complex DNA damage induced by irradiation.
Abstract: Monte Carlo simulations can classify DNA damage into different types and predict the amount of energy deposited. Geant4-DNA was used to predict simple and complex DNA damage induced by irradiation ...
2 citations
TL;DR: A perturbation expansion of the frequency of the model's nonzero modes is calculated, finding that approximating these modes with their unperturbed dynamics, as in a previous reduced order model, may not hold when the length of the DNA model increases.
Abstract: Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modeled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of conformational change in the model have been investigated and several reduced order models developed, the conformational dynamics as a function of the length of the oscillator chain is relatively less clear. To address this, we use a modified Lindstedt-Poincare method and numerical computations. We calculate a perturbation expansion of the frequency of the model's nonzero modes, finding that approximating these modes with their unperturbed dynamics, as in a previous reduced order model, may not hold when the length of the DNA model increases. We investigate the conformational change to the local perturbation in models of varying lengths, finding that for the chosen input and parameters, there are two regions of DNA length in the model - first, where the minimum energy required to undergo the conformational change increases with the DNA length; and second, where it is almost independent of the length of the DNA model. We analyze the conformational change in these models by adding randomness to the local perturbation, finding that the tendency of the system to remain in a stable conformation against random perturbation decreases with increase in DNA length. These results should help to understand the role of the length of a DNA molecule in influencing its conformational dynamics.
26 Feb 2020