Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices.

Network-based biocomputation (NBC) relies on accurate guiding of biological agents through nanofabricated channels produced by lithographic patterning techniques. Here, we report on the large-scale, wafer-level fabrication of optimized microfluidic channel networks (NBC networks) using electron-beam lithography as the central method. To confirm the functionality of these NBC networks, we solve an instance of a classical non-deterministic-polynomial-time complete ("NP-complete") problem, the subset-sum problem. The propagation of cytoskeletal filaments, e.g., molecular motor-propelled microtubules or actin filaments, relies on a combination of physical and chemical guiding along the channels of an NBC network. Therefore, the nanofabricated channels have to fulfill specific requirements with respect to the biochemical treatment as well as the geometrical confienement, with walls surrounding the floors where functional molecular motors attach. We show how the material stack used for the NBC network can be optimized so that the motor-proteins attach themselves in functional form only to the floor of the channels. Further optimizations in the nanolithographic fabrication processes greatly improve the smoothness of the channel walls and floors, while optimizations in motor-protein expression and purification improve the activity of the motor proteins, and therefore, the motility of the filaments. Together, these optimizations provide us with the opportunity to increase the reliability of our NBC devices. In the future, we expect that these nanolithographic fabrication technologies will enable production of large-scale NBC networks intended to solve substantially larger combinatorial problems that are currently outside the capabilities of conventional software-based solvers.

Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation.

Information processing by traditional, serial electronic processors consumes an ever-increasing part of the global electricity supply. An alternative, highly energy efficient, parallel computing paradigm is network-based biocomputation (NBC). In NBC a given combinatorial problem is encoded into a nanofabricated, modular network. Parallel exploration of the network by a very large number of independent molecular-motor-propelled protein filaments solves the encoded problem. Here we demonstrate a significant scale-up of this technology by solving four instances of Exact Cover, a nondeterministic polynomial time (NP) complete problem with applications in resource scheduling. The difficulty of the largest instances solved here is 128 times greater in comparison to the current state of the art for NBC.

Multiplication of Motor-Driven Microtubules for Nanotechnological Applications.

Microtubules gliding on motor-functionalized surfaces have been explored for various nanotechnological applications. However, when moving over large distances (several millimeters) and long times (tens of minutes), microtubules are lost due to surface detachment. Here, we demonstrate the multiplication of kinesin-1-driven microtubules that comprises two concurrent processes: (i) severing of microtubules by the enzyme spastin and (ii) elongation of microtubules by self-assembly of tubulin dimers at the microtubule ends. We managed to balance the individual processes such that the average length of the microtubules stayed roughly constant over time while their number increased. Moreover, we show microtubule multiplication in physical networks with topographical channel structures. Our method is expected to broaden the toolbox for microtubule-based in vitro applications by counteracting the microtubule loss from substrate surfaces. Among others, this will enable upscaling of network-based biocomputation, where it is vital to increase the number of microtubules during operation.

Gate Spacer Investigation for Improving the Speed of High-Frequency Carbon Nanotube-Based Field-Effect Transistors.

Carbon nanotube (CNT)-based field-effect transistors have demonstrated great potential for high-frequency (HF) analog transceiver electronics. Despite significant advancements, one of the remaining challenges is the optimization of the device architecture for obtaining the highest possible speed and linearity. While most studies so far have concentrated on symmetrical top gated FET devices, we report on the impact of the device architecture on their HF performance. Based on a wafer-level nanotechnology platform and device simulations, transistors with a buried gate having different widths and positions in the FET channel have been fabricated. Analysis of several FETs with nonsymmetrical gate electrode location in the channel revealed a speed increase of up to 18% measured by the external transit frequency fT and maximum frequency of oscillation fmax. Although only randomly oriented CNTs with a density of 25 CNTs/µm and 280 nm long channels were used in this study, transit frequencies up to 14 GHz were obtained.

Regeneration of Assembled, Molecular-Motor-Based Bionanodevices.

The guided gliding of cytoskeletal filaments, driven by biomolecular motors on nano/microstructured chips, enables novel applications in biosensing and biocomputation. However, expensive and time-consuming chip production hampers the developments. It is therefore important to establish protocols to regenerate the chips, preferably without the need to dismantle the assembled microfluidic devices which contain the structured chips. We here describe a novel method toward this end. Specifically, we use the small, nonselective proteolytic enzyme, proteinase K to cleave all surface-adsorbed proteins, including myosin and kinesin motors. Subsequently, we apply a detergent (5% SDS or 0.05% Triton X100) to remove the protein remnants. After this procedure, fresh motor proteins and filaments can be added for new experiments. Both, silanized glass surfaces for actin-myosin motility and pure glass surfaces for microtubule-kinesin motility were repeatedly regenerated using this approach. Moreover, we demonstrate the applicability of the method for the regeneration of nano/microstructured silicon-based chips with selectively functionalized areas for supporting or suppressing gliding motility for both motor systems. The results substantiate the versatility and a promising broad use of the method for regenerating a wide range of protein-based nano/microdevices.

Nanoscale switch for vortex polarization mediated by Bloch core formation in magnetic hybrid systems.

Vortices are fundamental magnetic topological structures characterized by a curling magnetization around a highly stable nanometric core. The control of the polarization of this core and its gyration is key to the utilization of vortices in technological applications. So far polarization control has been achieved in single-material structures using magnetic fields, spin-polarized currents or spin waves. Here we demonstrate local control of the vortex core orientation in hybrid structures where the vortex in an in-plane Permalloy film coexists with out-of-plane maze domains in a Co/Pd multilayer. The vortex core reverses its polarization on crossing a maze domain boundary. This reversal is mediated by a pair of magnetic singularities, known as Bloch points, and leads to the transient formation of a three-dimensional magnetization structure: a Bloch core. The interaction between vortex and domain wall thus acts as a nanoscale switch for the vortex core polarization.