Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor

In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule binding and triggering the impulse, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at fixed temperature. The resulting dynamics shows a Michaelis-Menten translocation velocity that depends on the chain flexibility. The scaling behavior of the mean translocation time with the polymer length for different bending values is also investigated.Comment: 10 pages, 10 figure

Translocation of a polymer chain driven by a dichotomous noise

We consider the translocation of a one-dimensional polymer through a pore channel helped by a motor driven by a dichotomous noise with time exponential correlation. We are interested in the study of the translocation time, mean velocity and stall force of the system as a function of the mean driving frequency. We find a monotonous translocation time, in contrast with the mean velocity which shows a pronounced maximum at a given frequency. Interestingly, the stall force shows a nonmonotonic behavior with the presence of a minimum. The influence of the spring elastic constant to the mean translocation times and velocities is also presented.Comment: 11 pages, 7 figure

Directional motion of forced polymer chains with hydrodynamic interaction

We study the propulsion of a one-dimensional (1D) polymer chain under sinusoidal external forces in the overdamped (low Reynolds number) regime. We show that, when hydrodynamical interactions are included, the polymer presents directional motion which depends on the phase differences of the external force applied along the chain. Moreover, the velocity shows a maximum as a function of the frequency. We discuss the relevance of all these results in light of recent nanotechnology experiments.Comment: 5 pages, 6 figure

Role of the central cations in the mechanical unfolding of DNA and RNA G-quadruplexes.

Cations are known to mediate diverse interactions in nucleic acids duplexes but they are critical in the arrangement of four-stranded structures. Here, we use all-atom molecular dynamics simulations with explicit solvent to analyse the mechanical unfolding of representative intramolecular G-quadruplex structures: a parallel, a hybrid and an antiparallel DNA and a parallel RNA, in the presence of stabilising cations. We confirm the stability of these conformations in the presence of [Formula: see text] central ions and observe distortions from the tetrad topology in their absence. Force-induced unfolding dynamics is then investigated. We show that the unfolding events in the force-extension curves are concomitant to the loss of coordination between the central ions and the guanines of the G-quadruplex. We found lower ruptures forces for the parallel configuration with respect to the antiparallel one, while the behaviour of the force pattern of the parallel RNA appears similar to the parallel DNA. We anticipate that our results will be essential to interpret the fine structure rupture profiles in stretching assays at high resolution and will shed light on the mechanochemical activity of G-quadruplex-binding machinery

Active polymer translocation in the three-dimensional domain

In this work we study the translocation process of a polymer through a nanochannel where a time dependent force is acting. Two conceptually different types of driving are used: a deterministic sinusoidal one and a random telegraph noise force. The mean translocation time presents interesting resonant minima as a function of the frequency of the external driving. For the computed sizes, the translocation time scales with the polymer length according to a power law with the same exponent for almost all the frequencies of the two driving forces. The dependence of the translocation time with the polymer rigidity, which accounts for the persistence length of the molecule, shows a different low frequency dependence for the two drivings

Transverse rectification of disorder-induced fluctuations in a driven system

We study numerically the overdamped motion of particles driven in a two dimensional ratchet potential. In the proposed design, of the so-called geometrical-ratchet type, the mean velocity of a single particle in response to a constant force has a transverse component that can be induced by the presence of thermal or other unbiased fluctuations. We find that additional quenched disorder can strongly enhance the transverse drift at low temperatures, in spite of reducing the transverse mobility. We show that, under general conditions, the rectified transverse velocity of a driven particle fluid is equivalent to the response of a one dimensional flashing ratchet working at a drive-dependent effective temperature, defined through generalized Einstein relations.Comment: 4.5 pages, 3 fig

End-pulled polymer translocation through a many-body flexible pore

This paper studies the features of a homopolymer translocating through a flexible pore. The channel is modeled as a monolayer tube composed by monomers with two elastic parameters: spring-like two body interaction and bending three body recall interaction. In order to guarantee the stability of the system, the membrane is compounded by a lipid bilayer structure having hydrophobic body (internal), while the pore is hydrophilic in both edges. The polymer is end-pulled from the cis-side to the trans-side by a cantilever, to which is connected through a spring able to measure the force acting on the polymer during the translocation. All the structure reacts to the impacts of the monomers of the polymer with vibrations generated by the movement of its constituent bodies. In these conditions, the work done by the cantilever shows a nonmonotonic behavior with the elastic constant, revealing a resonant-like behavior in a parameter region. Moreover, the force spectroscopy registered as a function of time, is able to record the main kinetics of the polymer progression inside the pore

Michaelis-Menten dynamics of a polymer chain out of a dichotomous ATP-based motor

We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The machine activation rate can be put in relationship with the available ATP concentration in the solution, which gives the necessary energy supply. The translocation time shows a monotonic behavior as a function of the activation frequency and the velocity follows a Michaelis-Menten law that arises naturally in this description. The estimation of the stall force of the motor follows a corrected Michaelis-Menten law which still is to be checked in experimental investigation. The results presented agree with recent biological experimental findings.Comment: 12 pages, 8 figure