In silico design and testing of guiding tracks for molecular shuttles powered by kinesin motors

Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots

Biological systems have evolved to harness non-equilibrium processes from the molecular to the macro scale. It is currently a grand challenge of chemistry, materials science, and engineering to understand and mimic biological systems that have the ability to autonomously sense stimuli, process these inputs, and respond by performing mechanical work. New chemical systems are responding to the challenge and form the basis for future responsive, adaptive, and active materials. In this article, we describe a particular biochemical-biomechanical network based on the microtubule cytoskeletal filament - itself a non-equilibrium chemical system. We trace the non-equilibrium aspects of the system from molecules to networks and describe how the cell uses this system to perform active work in essential processes. Finally, we discuss how microtubule-based engineered systems can serve as testbeds for autonomous chemical robots composed of biological and synthetic components.

Control of microtubule trajectory within an electric field by altering surface charge density

One of challenges for using microtubules (MTs) driven by kinesin motors in microfluidic environments is to control their direction of movement. Although applying physical biases to rectify MTs is prevalent, it has not been established as a design methodology in conjunction with microfluidic devices. In the future, the methodology is expected to achieve functional motor-driven nanosystems. Here, we propose a method to guide kinesin-propelled MTs in multiple directions under an electric field by designing a charged surface of MT minus ends labeled with dsDNA via a streptavidin-biotin interaction. MTs labeled with 20-bp or 50-bp dsDNA molecules showed significantly different trajectories according to the DNA length, which were in good agreement with values predicted from electrophoretic mobilities measured for their minus ends. Since the effective charge of labeled DNA molecules was equal to that of freely dispersed DNA molecules in a buffer solution, MT trajectory could be estimated by selecting labeling molecules with known charges. Moreover, the estimated trajectory enables to define geometrical sizes of a microfluidic device. This rational molecular design and prediction methodology allows MTs to be guided in multiple directions, demonstrating the feasibility of using molecular sorters driven by motor proteins.

Understanding the guiding of kinesin/microtubule-based microtransporters in microfabricated tracks

Microtransporters using cargo-laden microtubules propelled by kinesin motors are attractive for numerous applications in nanotechnology. To improve the efficiency of transport, the movement of microtubules must be guided by microfabricated tracks. However, the mechanisms of the guiding methods used are not fully understood. Here, using computer simulation, we systematically studied the guiding of such microtransporters by three different types of guiding methods: a chemical boundary, a physical barrier, and their combination. The simulation reproduced the probabilities of guiding previously observed experimentally for the three methods. Moreover, the simulation provided further insight into the mechanisms of guiding, which overturn previous assumptions and models.

In silico evolution of guiding track designs for molecular shuttles powered by kinesin motors

Molecular shuttles powered by kinesin motors require guiding tracks to perform specific tasks in nanoscale devices. Here, using our simulation of molecular shuttle movements, we describe an in silico evolutionary design method that makes it possible to automatically design the guiding tracks in accordance with their functions defined by designers. With this design method, we designed two types of pre-existing guiding track modules with improved performances, as well as one with a novel function.

Optimization of isopolar microtubule arrays

Isopolar arrays of aligned cytoskeletal filaments are components in a number of designs of hybrid nanodevices incorporating biomolecular motors. For example, a combination of filament arrays and motor arrays can form an actuator or a molecular engine resembling an artificial muscle. Here, isopolar arrays of microtubules are fabricated by flow alignment, and their quality is characterized by their degree of alignment. We find, in agreement with our analytical models, that the degree of alignment is ultimately limited by thermal forces, while the kinetics of the alignment process are influenced by the flow strength, the microtubule stiffness, the gliding velocity, and the tip length. Strong flows remove microtubules from the surface and reduce the filament density, suggesting that there is an optimal flow strength for the fabrication of ordered arrays.

Patterns of molecular motors that guide and sort filaments

Molecular motors can be immobilized to transport filaments and loads that are attached to these filaments inside a nano-device. However, if motors are distributed uniformly over a flat surface, the motility is undirected, and the filaments move equally in all directions. For many applications it is important to control the direction in which the filaments move, and two strategies have been explored to achieve this: applying external forces and confining the filaments inside channels. In this article, we discuss a third strategy in which the topography of the sample remains flat, but the motors are distributed non-uniformly over the surface. Systems of filaments and patterned molecular motors were simulated using a stochastic engine that included Brownian motion and filament bending elasticity. Using an evolutionary algorithm, patterns were optimized for their capacity to precisely control the paths of the filaments. We identified patterns of motors that could either direct the filaments in a particular direction, or separate short and long filaments. These functionalities already exceed what has been achieved with confinement. The patterns are composed of one or two types of motors positioned in lines or along arcs and should be easy to manufacture. Finally, these patterns can be easily combined into larger designs, allowing one to precisely control the motion of microscopic objects inside a device.

On-chip molecular communication: analysis and design

We consider a confined space molecular communication system, where molecules or information carrying particles are used to transfer information on a microfluidic chip. Considering that information-carrying particles can follow two main propagation schemes: passive transport, and active transport, it is not clear which achieves a better information transmission rate. Motivated by this problem, we compare and analyze both propagation schemes by deriving a set of analytical and mathematical tools to measure the achievable information rates of the on-chip molecular communication systems employing passive to active transport. We also use this toolbox to optimize design parameters such as the shape of the transmission area, to increase the information rate. Furthermore, the effect of separation distance between the transmitter and the receiver on information rate is examined under both propagation schemes, and a guidepost to design an optimal molecular communication setup and protocol is presented.

Nanoscale transport enables active self-assembly of millimeter-scale wires

Active self-assembly processes exploit an energy source to accelerate the movement of building blocks and intermediate structures and modify their interactions. A model system is the assembly of biotinylated microtubules partially coated with streptavidin into linear bundles as they glide on a surface coated with kinesin motor proteins. By tuning the assembly conditions, microtubule bundles with near millimeter length are created, demonstrating that active self-assembly is beneficial if components are too large for diffusive self-assembly but too small for robotic assembly.