Molecular Motor Transport through Hollow Nanowires

Lard, Mercy; Siethoff, Lasse ten; Generosi, Johanna; Månsson, Alf; Linke, Heiner

doi:10.1021/nl404714b

Cited by 33 publications

(28 citation statements)

References 33 publications

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“…(iii) Reduction of pass-junction error rates. We expect that this can be realized by simulationdriven design (such as described in SI Appendix, section S4), by evolutionary algorithms for designing the junction geometries (36, 37), or by using 3D geometries such as bridges or tunnels (38) which would offer zero error rates at pass junctions. (iv) To circumvent the inherent difficulties of tracking large numbers of individual filaments, automatic readout schemes at exits of interest can be used (39).…”

Section: Discussionmentioning

confidence: 99%

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Nicolau

Lard

Korten

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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131

216

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The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecularmotor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NPcomplete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.parallel computing | molecular motors | NP complete | biocomputation | nanotechnology M any combinatorial problems of practical importance, such as the design and verification of circuits (1), the folding (2) and design (3) of proteins, and optimal network routing (4), require that a large number of possible candidate solutions are explored in a brute-force manner to discover the actual solution. Because the time required for solving these problems grows exponentially with their size, they are intractable for conventional electronic computers, which operate sequentially, leading to impractical computing times even for medium-sized problems. Solving such problems therefore requires efficient parallel-computation approaches (5). However, the approaches proposed so far suffer from drawbacks that have prevented their implementation. For example, DNA computation, which generates mathematical solutions by recombining DNA strands (6, 7), or DNA static (8) or dynamic (9) nanostructures, is limited by the need for impractically large amounts of DNA (10-13). Quantum computation is limited in scale by decoherence and by the small number of qubits that can be integrated (14). Microfluidics-based parallel computation (15) is difficult to scale up in practice due to rapidly diverging physical size and complexity of the computation devices with the size of the problem, as well as the need for impractically large external pressure.Here, we propose a parallel-computation approach, which is based on encoding combinatorial problems into the geometry of a physical network of lithographically defined channels, followed by exploration of the network in a par...

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Section: Discussionmentioning

confidence: 99%

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Nicolau

Lard

Korten

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

131

216

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“…However, detachment of the cytoskeletal filaments from their tracks and thus interruption of guided transport cannot be entirely prevented. To overcome this limitation, transport through closed nanotubes has recently been explored …”

Section: Figurementioning

confidence: 98%

Controlled Retention and Release of Biomolecular Transport Systems Using Shape‐Changing Polymer Bilayers

et al. 2016

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Biomolecular transport systems based on cytoskeletal filaments and motor proteins have become promising tools for aw ide range of nanotechnological applications.I n this paper,w er eport control of such transport systems using substrates with switchables hape.W ed emonstrate this approach on the example of microtubules gliding on surfaces of self-folding polymer bilayers with adsorbed kinesin motors. The polymer bilayers are able to undergo reversible transitions between flat and tube-like shapes that allowt he externally controlled retention and release of gliding microtubules.T he demonstrated approach, based on surfaces with reconfigurable topography,opens broad perspectives to control biomolecular transport systems for bioanalytical and sensing applications,as well as for the construction of subcellular compartments in the field of synthetic biology.

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“…47 It is also amenable to single-molecule studies where one would like to, for example, observe protein motors moving along DNA, now without an external force acting on the protein. 51 Using NCs with open top slits will allow for continuous ATP supply along long channels, 52,53 including the capability to turn motors on and off. 49,50 Furthermore, NCs of diameter ≈100 nm can be used to study actomyosin motility in a 3D configuration similar to that in the sarcomere (and unlike the planar configuration of traditional motility assays), as recently demonstrated in hollow nanowires.…”

Section: Nanoscale Papermentioning

confidence: 99%

Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

et al. 2014

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Synthetic molecular motors typically take nanometer-scale steps through rectification of thermal motion. Here we propose Inchworm, a DNA-based motor that employs a pronounced power stroke to take micrometer-scale steps on a time scale of seconds, and we design, fabricate, and analyze the nanofluidic device needed to operate the motor. Inchworm is a kbp-long, double-stranded DNA confined inside a nanochannel in a stretched configuration. Motor stepping is achieved through externally controlled changes in salt concentration (changing the DNA's extension), coordinated with ligand-gated binding of the DNA's ends to the functionalized nanochannel surface. Brownian dynamics simulations predict that Inchworm's stall force is determined by its entropic spring constant and is ∼ 0.1 pN. Operation of the motor requires periodic cycling of four different buffers surrounding the DNA inside a nanochannel, while keeping constant the hydrodynamic load force on the DNA. We present a two-layer fluidic device incorporating 100 nm-radius nanochannels that are connected through a few-nm-wide slit to a microfluidic system used for in situ buffer exchanges, either diffusionally (zero flow) or with controlled hydrodynamic flow. Combining experiment with finite-element modeling, we demonstrate the device's key performance features and experimentally establish achievable Inchworm stepping times of the order of seconds or faster.

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Molecular Motor Transport through Hollow Nanowires

Cited by 33 publications

References 33 publications

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Parallel computation with molecular-motor-propelled agents in nanofabricated networks

Controlled Retention and Release of Biomolecular Transport Systems Using Shape‐Changing Polymer Bilayers

Fluidic switching in nanochannels for the control of Inchworm: a synthetic biomolecular motor with a power stroke

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