相关论文: Velocity and processivity of helicase unwinding of…

DEAD-box RNA helicases (DDXs) are essential RNA metabolism regulators that typically unwind dsRNA in an ATP-dependent manner. However, recent studies show some DDXs can also unwind dsRNA without ATP, a phenomenon that remains poorly…

We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…

The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…

In bulk ferroelectric liquid crystals, the molecular director twists in a helix. In narrow cells, this helix can be unwound by an applied electric field or by boundary effects. To describe helix unwinding as a function of both electric…

We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…

We utilize resolvent and weakly nonlinear analyses in combination with direct numerical simulations (DNS) to identify mechanisms for oblique transition in a Mach 5 hypersonic flow over an adiabatic slender double-wedge. Even though the…

Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…

Particle transport through an open, discrete 1-D channel against a mechanical or chemical bias is analyzed within a master equation approach. The channel, externally driven by time dependent site energies, allows multiple occupation due to…

The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…

Some types of bacteria use rotating helical flagella to swim. The motion of such organisms takes place in the regime of low Reynolds numbers where viscous effects dominate and where the dynamics is governed by hydrodynamic interactions.…

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…

In chemical reactions, trajectories typically turn from reactants to products when crossing a dividing surface close to the normally hyperbolic invariant manifold (NHIM) given by the intersection of the stable and unstable manifolds of a…

While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…

The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…

We study the conservative and deterministic dynamics of two nonlinearly interacting particles evolving in a one-dimensional spatially periodic washboard potential. A weak tilt of the washboard potential is applied biasing one direction for…

The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…

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…

The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…

In this paper we study a new class of shell models, defined in terms of two complex dynamical variables per shell, transporting positive and negative helicity respectively. The dynamical equations are derived from a decomposition into…

The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…