Showing papers on "Molecular models of DNA published in 2021"

Computational and numerical simulations for the deoxyribonucleic acid (DNA) model

Abstract: In this research paper, the modified Khater method, the Adomian decomposition method, and B-spline techniques (cubic, quintic, and septic) are applied to the deoxyribonucleic acid (DNA) model to get the analytical, semi-analytical, and numerical solutions. These solutions comprise much information about the dynamical behavior of the homogenous long elastic rods with a circular section. These rods constitute a pair of the polynucleotide rods of the DNA molecule which are plugged by an elastic diaphragm that demonstrates the hydrogen bond's role in this communication. The stability property is checked for some solutions to show more effective and powerful of obtained solutions. Based on the role of analytical and semi-analytical techniques in the motivation of the numerical techniques to be more accurate, the B-spline numerical techniques are applied by using the obtained exact solutions on the DNA model to show which one of them is more accurate than other, to explain more of the dynamic behavior of the homogenous long elastic rods, and to show the coincidence between the different types of obtained solutions. The obtained solutions verified with Maple 16 & Mathematica 12 by placing them back into the original equations. The performance of these methods shows the power and effectiveness of them for applying to many different forms of the nonlinear evolution equations with an integer and fractional order.

Abundant exact closed-form solutions and solitonic structures for the double-chain deoxyribonucleic acid (DNA) model

Abstract: In this work, the abundant exact closed-form solutions and dynamics of solitons for the double-chain deoxyribonucleic acid (DNA) model is obtained by utilizing the generalized exponential rational function (GERF) method. Deoxyribonucleic acid (DNA) retains the genetic information that creatures need to live and reproduce themselves. We obtained several novel exact soliton and exponential rational functional solutions in the shapes of dynamics of solitons like multi-solitons, breather-type solitons, abundant elastic interactions between multi-solitons, and nonlinear waves, oscillating multi-solitons, and Lump solitons. These derived solutions were never reported in the literature. The dynamical structures of some exact solitons are exhibited graphically by assigning suitable values to the free parameters via 3D figures. The generated solutions can be more useful and help to explain the internal interactions of the double-chain DNA model. The symbolic computational work and the obtained solutions show that the present proposed GERF method is effective, robust, and straightforward. Moreover, these types of higher-order NLEEs can be solved using the current technique.

Optimizing the dynamic and thermodynamic properties of hybridization in DNA-mediated nanoparticle self-assembly.

Abstract: DNA-directed nanoparticle (DNA–NP) systems provide various applications in sensing, medical diagnosis, data storage, plasmonics and photovoltaics. Bonding probability and melting properties are helpful to evaluate the selectivity, thermostability and thermosensitivity of these applications. We investigated the influence of temperature, nanoparticle size, DNA chain length and surface grafting density of DNA on one nanoparticle on the DNA dynamic hybridization percentage and melting properties of DNA–NP assembly systems by molecular dynamics simulation. The high degree of consistency of free energy estimations for DNA hybridization via our theoretical deduction and the nearest-neighbor rule generally used in experiments validates reasonably our DNA model. The melting temperature and thermosensitivity parameter are determined by the sigmoidal melting curves based on hybridization percentage versus temperature. The results indicated that the hybridization percentage presents a downward trend with increasing temperature and nanoparticle size. Applications based on DNA–NP systems with bigger nanoparticle size, such as DNA probes, have better selectivity, thermostability and thermosensitivity. There exist optimal DNA chain length and surface grafting density where the hybridization percentage reaches the maximal value. The melting temperature reaches a maximum at the point of optimal grafting density, while the thermosensitivity parameter presents an upward trend with the increase of grafting density. Several physical quantities consisting of the radial density function, root mean square end-to-end distance, contact distance parameter and effective volume fraction are used to analyse DNA chain conformations and DNA–NP packing in the assembly process. Our findings provide the theoretical basis for the improvement and optimization of applications based on DNA–NP systems.

Efimov-DNA Phase diagram: three stranded DNA on a cubic lattice

Abstract: We define a generalised model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modelled by random walks on the three-dimensional cubic lattice with different interactions between two chains of the same type and two chains of different types. This model may be thought of as a classical analogue of the quantum three-body problem. In the quantum situation it is known that three identical quantum particles will form a triplet with an infinite tower of bound states at the point where any pair of particles would have zero binding energy. The phase diagram is mapped out, and the different phase transitions examined using finite-size scaling. We look particularly at the scaling of the DNA model at the equivalent Efimov point for chains up to 10000 steps in length. We find clear evidence of several bound states in the finite-size scaling. We compare these states with the expected Efimov behaviour.

Efimov-DNA phase diagram: Three stranded DNA on a cubic lattice.

Abstract: We define a generalized model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modeled by random walks on the three-dimensional cubic lattice with different interactions between two chains of the same type and two chains of different types. This model may be thought of as a classical analog of the quantum three-body problem. In the quantum situation, it is known that three identical quantum particles will form a triplet with an infinite tower of bound states at the point where any pair of particles would have zero binding energy. The phase diagram is mapped out, and the different phase transitions are examined using finite-size scaling. We look particularly at the scaling of the DNA model at the equivalent Efimov point for chains up to 10 000 steps in length. We find clear evidence of several bound states in the finite-size scaling. We compare these states with the expected Efimov behavior.

Implications of the quantum DNA model for information sciences

Abstract: The DNA molecule can be modeled as a quantum logic processor, and this model has been supported by pilot research that experimentally demonstrated non-local communication between cells in separated cell cultures. This modeling and pilot research have important implications for information sciences, providing a potential architecture for quantum computing that operates at room temperature and is scalable to millions of qubits, and including the potential for an entanglement communication system based upon the quantum DNA architecture. Such a system could be used to provide non-local quantum key distribution that could not be blocked by any shielding or water depth, would be simultaneous over any distance, and could not be electromagnetically interfered with or eavesdropped upon. The quantum DNA model also has implications for artificial neural networks and can provide architecture for a system of quantum random number generation.