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Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices

Meinecke, Christoph R. ; Heldt, Georg ; Blaudeck, Thomas ; Lindberg, Frida W. LU ; van Delft, Falco C.M.J.M. ; Rahman, Mohammad Ashikur ; Salhotra, Aseem ; Månsson, Alf LU ; Linke, Heiner LU orcid and Korten, Till , et al. (2023) In Materials 16(3).
Abstract

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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
electron-beam lithography, microfluidics, molecular motors, nanotechnology, network-based biocomputation
in
Materials
volume
16
issue
3
article number
1046
publisher
MDPI AG
external identifiers
  • scopus:85147912364
  • pmid:36770052
ISSN
1996-1944
DOI
10.3390/ma16031046
language
English
LU publication?
yes
id
0bdd2bc9-7d1f-4f72-adce-19f6106a0a7f
date added to LUP
2023-03-06 12:55:32
date last changed
2024-06-25 09:55:25
@article{0bdd2bc9-7d1f-4f72-adce-19f6106a0a7f,
  abstract     = {{<p>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.</p>}},
  author       = {{Meinecke, Christoph R. and Heldt, Georg and Blaudeck, Thomas and Lindberg, Frida W. and van Delft, Falco C.M.J.M. and Rahman, Mohammad Ashikur and Salhotra, Aseem and Månsson, Alf and Linke, Heiner and Korten, Till and Diez, Stefan and Reuter, Danny and Schulz, Stefan E.}},
  issn         = {{1996-1944}},
  keywords     = {{electron-beam lithography; microfluidics; molecular motors; nanotechnology; network-based biocomputation}},
  language     = {{eng}},
  number       = {{3}},
  publisher    = {{MDPI AG}},
  series       = {{Materials}},
  title        = {{Nanolithographic Fabrication Technologies for Network-Based Biocomputation Devices}},
  url          = {{http://dx.doi.org/10.3390/ma16031046}},
  doi          = {{10.3390/ma16031046}},
  volume       = {{16}},
  year         = {{2023}},
}