Related papers: Periodically driven DNA: Theory and simulation
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…
We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force…
We consider an unpinned chain of harmonic oscillators with periodic boundary conditions, whose dynamics is perturbed by a random flip of the sign of the velocities. The dynamics conserves the total volume (or elongation) and the total…
We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
A new class of models based on hysteresis functions is developed to describe atomic force microscopes operating in dynamic mode. Such models are able to account for dissipative phenomena in the tip-sample interaction which are peculiar of…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the worm-like chain…
We apply imaginary-time evolution, ${\rm e}^{-\tau H}$, to study relaxation dynamics of gapless quantum antiferromagnets described by the spin-rotation invariant Heisenberg Hamiltonian ($H$). Using quantum Monte Carlo simulations, we…
We investigate the coherent transport properties of a DNA chain on a substrate which is subjected to a uniform electric field perpendicular to the surface. On the basis of the effective tight-binding model which simulates charge transport…
We studied the electrical conductivity of DNA samples as function of the number of DNA molecules. We showed that the insulating gap (no current at low voltage) increases from ~1-2 V for bundles and large ropes to ~4-7 V for few DNA…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Stochastic driven flow along a channel can be modeled by the asymmetric simple exclusion process. We confirm numerically the presence of a dynamic queuing phase transition at a nonzero obstruction strength, and establish its scaling…
The natural impedance, or dynamic relationship between force and motion, of a human operator can determine the stability of exoskeletons that use interaction-torque feedback to amplify human strength. While human impedance is typically…
The sliding friction of a dimer moving over a periodic substrate and subjected to an external force is studied in the steady state for arbitrary temperatures within a one-dimensional model. Nonlinear phenomena that emerge include dynamic…
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…
We introduce a simple model for DNA evolution. Using the method of Peng et al.$^1$, we investigate the fractal properties of the system. For small chains and chains of intermediate size we find a fractal exponent that indicates the…
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…