Related papers: dsDNA persistence length with divalent ions
Using a combination of high-level ab initio electronic structure methods with efficient on-the-fly semiclassical evaluation of nuclear dynamics, we performed a massive scan of small polyatomic molecules searching for a long lasting…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
Experiments reveal that DNA solvation dynamics (SD) is characterized by multiple time scales ranging from a few ps to hundreds of ns and in some cases even up to microseconds. The last part of decay is slow and is characterized by a power…
We present the concluding result from an Ives-Stilwell-type time dilation experiment using 7Li+ ions confined at a velocity of beta = v/c = 0.338 in the storage ring ESR at Darmstadt. A Lambda-type three-level system within the hyperfine…
We derive an expression for the static dielectric constant of the colloidal susp ensions based on the electrokinetic equations. The analysis assumes that the ions have the same diffusivity, and that the double layer is much thinner than the…
We implement a technique to characterize electromagnetic properties at frequencies 100 to 165 GHz (3 cm$^{-1}$ to 4.95 cm$^{-1}$) of oriented montmorillionite samples using an open cavity resonator connected to a sub-millimeter wave VNA…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
The interaction between charged objects in an electrolyte solution is a fundamental question in soft matter physics. It is well-known that the electrostatic contribution to the interaction energy decays exponentially with object separation.…
Ion distributions in dilute polyelectrolyte solutions are studied by means of Langevin dynamics simulations. We show that the distributions depend on the conformation of a chain while the conformation is determined by the chain stiffness…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
The thermodynamics of nucleic acid processes is heavily affected by the electric double-layer of micro-ions around the polyions. We focus here on the Coulombic contribution to the salt-polyelectrolyte preferential interaction (Donnan)…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
In order to study the molecular damage induced in the form of single-strand and double-strand breaks by the ionizing radiation at the DNA level, Geant4-DNA Monte Carlo simulation code for complete transportation of primary protons and other…
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…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
In this paper, we have studied, within a discrete WLC model, the spatial constraints in magnetic tweezers used in single molecule experiments. Two elements are involved: first, the fixed plastic slab on which is stuck the initial strand,…
Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to…