Related papers: DNA mechanical deformations and chiral spin select…
The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are…
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one of the signatures of this chirality, the coupling between stretch and twist deformations. We show that the extension of a…
The structure of DNA in the nucleosome core particle is studied using an elastic model that incorporates anisotropy in the bending energetics and twist-bend coupling. Using the experimentally determined structure of nucleosomal DNA [T.J.…
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a…
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…
Because of the double-helical structure of DNA, in which two strands of complementary nucleotides intertwine around each other, a covalently closed DNA molecule with no interruptions in either strand can be viewed as two interlocked…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
The theoretical study of deformability of special sequence of DNA double helix TATA-box is presentated. The paper elaborates on the mechanisms of abnormal deformation of DNA TATA-box double helix that cannot be explained using the standard…
We theoretically analyze spin filtering in two-terminal systems, induced by the spin-orbit interaction (SOI), as a possible origin of the ``chirality-induced spin selectivity'' (CISS) effect observed experimentally in chiral molecules, such…
In contrast to the sequence dependent elasticity of the DNA strand, which is revealed as nonlocal and nonlinear, the geometric constraints derived by differential geometry have not been fully elaborated in DNA strand dynamics, even though…
Quantun spin transport through a short DNA chain connected to ferromagnetic electrodes has been investigated by the transfer matrix method. We describe the system by a tight-binding model where the parameters are extracted from the…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
Chiral-induced-spin-selectivity of electron transport and its interplay with DNA's mechanical motion is explored in a double stranded DNA helix with spin-orbit-coupling. The mechanical degree of freedom is treated as a stochastic classical…
We report on a way to manipulate the spin transport through double-stranded DNA contacted by normal-metal electrodes. On the basis of an effective model Hamiltonian, the conductance and the spin polarization are calculated in the presence…
The measured electric resistance of carbon nanotubes wrapped with DNA molecules depends strongly on the spin of the injected electrons. Motivated by these experiments, we study the effect of helix-shaped potentials on the electronic…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the…
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:…