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Design of network-b...
Design of network-based biocomputation circuits for the exact cover problem
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- Korten, Till (author)
- Dresden University of Technology
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- Diez, Stefan (author)
- Dresden University of Technology,Max Planck Institute of Molecular Cell Biology and Genetics
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- Linke, Heiner (author)
- Lund University,Lunds universitet,NanoLund: Centre for Nanoscience,Annan verksamhet, LTH,Lunds Tekniska Högskola,Fasta tillståndets fysik,Fysiska institutionen,Institutioner vid LTH,Other operations, LTH,Faculty of Engineering, LTH,Solid State Physics,Department of Physics,Departments at LTH,Faculty of Engineering, LTH
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- Nicolau, Jr., Dan V. (author)
- Queensland University of Technology
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- Kugler, Hillel (author)
- Bar-Ilan University
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(creator_code:org_t)
- 2021-08-12
- 2021
- English.
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 23:8
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Abstract
Subject headings
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- Exact cover is a non-deterministic polynomial time (NP)-complete problem that is central to optimization challenges such as airline fleet planning and allocation of cloud computing resources. Solving exact cover requires the exploration of a solution space that increases exponentially with cardinality. Hence, it is time- and energy consuming to solve large instances of exact cover by serial computers. One approach to address these challenges is to utilize the inherent parallelism and high energy efficiency of biological systems in a network-based biocomputation (NBC) device. NBC is a parallel computing paradigm in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. The network is then explored in parallel using a large number of biological agents, such as molecular-motor-propelled protein filaments. The answer to the combinatorial problem can then be inferred by measuring the positions through which the agents exit the network. Here, we (i) show how exact cover can be encoded and solved in an NBC device, (ii) define a formalization that allows to prove the correctness of our approach and provides a mathematical basis for further studying NBC, and (iii) demonstrate various optimizations that significantly improve the computing performance of NBC. This work lays the ground for fabricating and scaling NBC devices to solve significantly larger combinatorial problems than have been demonstrated so far.
Subject headings
- NATURVETENSKAP -- Biologi -- Biofysik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biophysics (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Elektroteknik och elektronik -- Datorsystem (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Electrical Engineering, Electronic Engineering, Information Engineering -- Computer Systems (hsv//eng)
- NATURVETENSKAP -- Fysik -- Annan fysik (hsv//swe)
- NATURAL SCIENCES -- Physical Sciences -- Other Physics Topics (hsv//eng)
Keyword
- Biological computation
- Exact cover
- Network based biocomputation
- NP-complete problems
Publication and Content Type
- art (subject category)
- ref (subject category)
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