相关论文: Role of helicity in DNA hairping folding dynamics

By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp…

Helicity is a quadratic invariant of the Euler equation in three dimensions. As the energy, when present helicity cascades to smaller scales where it dissipates. However, the role played by helicity in the energy cascade is still unclear.…

We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…

The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…

The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…

The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…

Helical magnetic background fields with adjustable pitch angle are imposed on a conducting fluid in a differentially rotating cylindrical container. The small-scale kinetic and current helicities are calculated for various field geometries,…

We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…

Unusually high bending flexibility has been recently reported for DNA on short length scales. We use atomic force microscopy (AFM) in solution to obtain a direct estimate of DNA bending statistics for scales down to one helical turn. It…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

The evolution of magnetic fields is studied using simulations of forced helical turbulence with strong imposed shear. After some initial exponential growth, the magnetic field develops a large scale travelling wave pattern. The resulting…

We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…

The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…

The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…

We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…

A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…

A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…