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The equilibrium structure of a Dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We studied the structure and mechanical properties of DNA i-motif nanowires by means of molecular dynamics computer simulations. We built up to 230 nm long nanowires, based on a repeated TC5 sequence from crystallographic data, fully…
The Kirchhoff elastic theory of thin filaments with spontaneous curvature is employed in the understanding of the onset of the kink transitions observed in short DNA rings. Dynamical analysis shows that when its actual curvature is less…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
Organization and maintenance of the chromosomal DNA in living cells strongly depends on the DNA interactions with a plethora of DNA-binding proteins. Single-molecule studies show that formation of nucleoprotein complexes on DNA by such…
Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…
Debates about conductivity of DNAs have been recently renewed due to contradictory results of direct measurements by use of electrical contacts to molecules. In several works it was discovered that double-stranded (ds)DNAs are conductors:…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to…
Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is…