Stochastic analysis of the motion of DNA nanomechanical bipeds

Self-repelling bipedal exploration process

A self-repelling two-leg (biped) spider walk is considered where the local stochastic movements are governed by two independent control parameters β_{d} and β_{h}, so that the former controls the distance (d) between the legs positions, and the latter controls the statistics of self-crossing of the traversed paths. The probability measure for local movements is supposed to be the one for the "true self-avoiding walk" multiplied by a factor exponentially decaying with d. After a transient behavior for short times, a variety of behaviors have been observed for large times depending on the value of β_{d} and β_{h}. Our statistical analysis reveals that the system undergoes a crossover between two (small and large β_{d}) regimes identified in large times (t). In the small β_{d} regime, the random walkers (identified by the position of the legs of the spider) remain on average in a fixed nonzero distance in the large time limit, whereas in the second regime (large β_{d}), the absorbing force between the walkers dominates the other stochastic forces. In the latter regime, d decays in a power-law fashion with the logarithm of time. When the system is mapped to a growth process (represented by a height field which is identified by the number of visits for each point), the roughness and the average height show different behaviors in two regimes, i.e., they show a power law with respect to t in the first regime and logt in the second regime. The fractal dimension of the random walker traces and the winding angle are shown to consistently undergo a similar crossover.

First-passage properties of molecular spiders

Molecular spiders are synthetic catalytic DNA-based nanoscale walkers. We study the mean first-passage time for abstract models of spiders moving on a finite two-dimensional lattice with various boundary conditions and compare it with the mean first-passage time of spiders moving on a one-dimensional track. We evaluate by how much the slowdown on newly visited sites, owing to catalysis, can improve the mean first-passage time of spiders and show that in one dimension, when both ends of the track are an absorbing boundary, the performance gain is lower than in two dimensions, when the absorbing boundary is a circle; this persists even when the absorbing boundary is a single site.

Superdiffusive transport by multivalent molecular walkers moving under load

We introduce a model for translational molecular motors to demonstrate that a multivalent catalytic walker with flexible, uncoordinated legs can transform the free energy of surface-bound substrate sites into mechanical work and undergo biased, superdiffusive motion, even in opposition to an external load force. The walker in the model lacks any inherent orientation of body or track, and its legs have no chemomechanical coupling other than the passive constraint imposed by their connection to a common body. Yet, under appropriate kinetic conditions, the walker's motion is biased in the direction of unvisited sites, which allows the walker to move nearly ballistically away from the origin as long as a local supply of unmodified substrate sites is available. The multivalent random walker model is mathematically formulated as a continuous-time Markov process and is studied numerically. We use Monte Carlo simulations to generate ensemble estimates of the mean squared displacement and mean work done for this nonergodic system. Our results show that a residence time bias between visited and unvisited sites leads to superdiffusive motion over significant times and distances. This mechanism can be used to adapt any enzyme-substrate system with appropriate kinetics for use as a functional chemical implementation of a molecular motor, without the need for structural anisotropy or conformationally mediated chemomechanical coordination.

Molecular spiders on a plane

Synthetic biomolecular spiders with "legs" made of single-stranded segments of DNA can move on a surface covered by single-stranded segments of DNA called substrates when the substrate DNA is complementary to the leg DNA. If the motion of a spider does not affect the substrates, the spider behaves asymptotically as a random walk. We study the diffusion coefficient and the number of visited sites for spiders moving on the square lattice with a substrate in each lattice site. The spider's legs hop to nearest-neighbor sites with the constraint that the distance between any two legs cannot exceed a maximal span. We establish analytic results for bipedal spiders, and investigate multileg spiders numerically. In experimental realizations legs usually convert substrates into products (visited sites). The binding of legs to products is weaker, so the hopping rate from the substrates is smaller. This makes the problem non-Markovian and we investigate it numerically. We demonstrate the emergence of a counterintuitive behavior-the more spiders are slowed down on unvisited sites, the more motile they become.