Simulating molecular shuttle movements: Towards computer-aided design of nanoscale transport systems

Abstract

Molecular shuttles based on the motor protein kinesin and microtubule filaments have the potential to extend the lab-on-a-chip paradigm to nanofluidics by enabling the active, directed and selective transport of molecules and nanoparticles. Based on experimentally determined parameters, in particular the trajectory persistence length of a microtubule gliding on surface-adhered kinesin motors, we developed a Monte-Carlo simulation, which models the transport properties of guiding structures, such as channels, rectifiers and concentrators, and reproduces the properties of several experimentally realized systems. Our tool facilitates the rational design of individual guiding structures as well as whole networks, and can be adapted to the simulation of other nanoscale transport systems.

Information Rates of Active Propagation in Microchannel Molecular Communication

“…In [12], these values were given as v avg = 0.85 µm/s, D = 2.0 · 10 −3 µm 2 /s, and L p = 111 µm. Following [12], in case of a collision with a boundary, we assume that the microtubule sets θ i so as to follow the boundary.…”

“…The motion of the microtubule is largely regular, although the effects of Brownian motion cause random fluctuations. We use a simulation scheme from [12], noting that microtubules stick to the motor-lined surface, so a two-dimensional discrete-time simulation is sufficient. In this case,…”

Quick system design of vesicle-based active transport molecular communication by using a simple transport model

“…Following [20], in case of a collision with a boundary, we assume that the microtubule does not reflect off the boundary, as in an elastic collision, but instead sets θ i so as to follow the boundary. The starting location of the microtubule is assumed to be random and uniformly distributed across the entire propagation area.…”

“…Therefore, previous works have relied on computer simulations to study these systems. In [20,19] the motion of microtubule filaments over stationary kinesin molecular motors was simulated and in [9,10] a complete simulation of the communication system was presented. In this work, for our simulation based results, we use the same simulation techniques proposed in [10].…”

Protein Linear Molecular Motor‐Powered Nanodevices

“…In fact, progress in this area has reached the extent that simulations, or in silico design tools, are being developed that reduce the need for expensive e-beam lithographed prototypes. [42] Essentially, planar devices address the problem of continuous operation of nanodevices based on protein molecular motors. Indeed, most of the 'single dimension' devices described above (bar the natural or hypothetical bi-directional devices) cannot continuously operate as the unidirectional movement has to stop when the motile element (e.g., microtubule or bead) reaches the end of the micro/nano-fabricated pathway.…”