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Traditional scientific modeling typically begins with fixed, instance-wise effective equations and then carries out equation-specific analysis and computation, a procedure that becomes exceptionally challenging in complex applications such…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Temperature-induced phase transition in BaTiO3 has been explored using the machine learning analysis of domain morphologies visualized via variable-temperature scanning transmission electron microscopy (STEM) imaging data. This approach is…
Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…