Literature DB >> 26903637

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

Dan V Nicolau7, Mercy Lard2, Till Korten3, Falco C M J M van Delft4, Malin Persson5, Elina Bengtsson5, Alf Månsson5, Stefan Diez3, Heiner Linke6, Dan V Nicolau7.   

Abstract

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, molecular-motor-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 NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

Keywords:  NP complete; biocomputation; molecular motors; nanotechnology; parallel computing

Year:  2016        PMID: 26903637      PMCID: PMC4791004          DOI: 10.1073/pnas.1510825113

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  39 in total

1.  Protein design is NP-hard.

Authors:  Niles A Pierce; Erik Winfree
Journal:  Protein Eng       Date:  2002-10

Review 2.  Studying kinesin motors by optical 3D-nanometry in gliding motility assays.

Authors:  Bert Nitzsche; Volker Bormuth; Corina Bräuer; Jonathon Howard; Leonid Ionov; Jacob Kerssemakers; Till Korten; Cecile Leduc; Felix Ruhnow; Stefan Diez
Journal:  Methods Cell Biol       Date:  2010       Impact factor: 1.441

3.  Fungi use efficient algorithms for the exploration of microfluidic networks.

Authors:  Kristi L Hanson; Dan V Nicolau; Luisa Filipponi; Lisen Wang; Abraham P Lee; Dan V Nicolau
Journal:  Small       Date:  2006-10       Impact factor: 13.281

4.  Tracking single particles and elongated filaments with nanometer precision.

Authors:  Felix Ruhnow; David Zwicker; Stefan Diez
Journal:  Biophys J       Date:  2011-06-08       Impact factor: 4.033

5.  Computing with DNA.

Authors:  D Beaver
Journal:  J Comput Biol       Date:  1995       Impact factor: 1.479

6.  Complexity of protein folding.

Authors:  A S Fraenkel
Journal:  Bull Math Biol       Date:  1993-11       Impact factor: 1.758

7.  Molecular computation of solutions to combinatorial problems.

Authors:  L M Adleman
Journal:  Science       Date:  1994-11-11       Impact factor: 47.728

8.  Kinesin takes one 8-nm step for each ATP that it hydrolyzes.

Authors:  D L Coy; M Wagenbach; J Howard
Journal:  J Biol Chem       Date:  1999-02-05       Impact factor: 5.157

9.  Silanized surfaces for in vitro studies of actomyosin function and nanotechnology applications.

Authors:  Mark Sundberg; Jenny P Rosengren; Richard Bunk; Joakim Lindahl; Ian A Nicholls; Sven Tågerud; Pär Omling; Lars Montelius; Alf Månsson
Journal:  Anal Biochem       Date:  2003-12-01       Impact factor: 3.365

10.  Tracking actomyosin at fluorescence check points.

Authors:  Mercy Lard; Lasse ten Siethoff; Alf Månsson; Heiner Linke
Journal:  Sci Rep       Date:  2013-01-21       Impact factor: 4.379

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  28 in total

Review 1.  From isolated structures to continuous networks: A categorization of cytoskeleton-based motile engineered biological microstructures.

Authors:  Rachel Andorfer; Joshua D Alper
Journal:  Wiley Interdiscip Rev Nanomed Nanobiotechnol       Date:  2019-02-11

2.  Reversible signal transmission in an active mechanical metamaterial.

Authors:  Alexander P Browning; Francis G Woodhouse; Matthew J Simpson
Journal:  Proc Math Phys Eng Sci       Date:  2019-07-24       Impact factor: 2.704

3.  Reply to Einarsson: The computational power of parallel network exploration with many bioagents.

Authors:  Dan V Nicolau; Mercy Lard; Till Korten; Falco C M J M van Delft; Malin Persson; Elina Bengtsson; Alf Månsson; Stefan Diez; Heiner Linke; Dan V Nicolau
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-25       Impact factor: 11.205

4.  New biological device not faster than regular computer.

Authors:  Jonas Einarsson
Journal:  Proc Natl Acad Sci U S A       Date:  2016-05-25       Impact factor: 11.205

Review 5.  Synchronous operation of biomolecular engines.

Authors:  Jakia Jannat Keya; Arif Md Rashedul Kabir; Akira Kakugo
Journal:  Biophys Rev       Date:  2020-03-03

Review 6.  Non-equilibrium assembly of microtubules: from molecules to autonomous chemical robots.

Authors:  H Hess; Jennifer L Ross
Journal:  Chem Soc Rev       Date:  2017-09-18       Impact factor: 54.564

7.  Positional Isomers of a Non-Nucleoside Substrate Differentially Affect Myosin Function.

Authors:  Mike Woodward; Eric Ostrander; Seung P Jeong; Xiarong Liu; Brent Scott; Matt Unger; Jianhan Chen; Dhandapani Venkataraman; Edward P Debold
Journal:  Biophys J       Date:  2020-06-30       Impact factor: 4.033

8.  Optical control of fast and processive engineered myosins in vitro and in living cells.

Authors:  Paul V Ruijgrok; Rajarshi P Ghosh; Sasha Zemsky; Muneaki Nakamura; Rui Gong; Lin Ning; Robert Chen; Vipul T Vachharajani; Alexander E Chu; Namrata Anand; Raphael R Eguchi; Po-Ssu Huang; Michael Z Lin; Gregory M Alushin; Jan T Liphardt; Zev Bryant
Journal:  Nat Chem Biol       Date:  2021-02-18       Impact factor: 15.040

9.  Myosin-Induced Gliding Patterns at Varied [MgATP] Unveil a Dynamic Actin Filament.

Authors:  Elina Bengtsson; Malin Persson; Mohammad A Rahman; Saroj Kumar; Hideyo Takatsuki; Alf Månsson
Journal:  Biophys J       Date:  2016-10-04       Impact factor: 4.033

10.  Mechanical splitting of microtubules into protofilament bundles by surface-bound kinesin-1.

Authors:  Virginia VanDelinder; Peter G Adams; George D Bachand
Journal:  Sci Rep       Date:  2016-12-21       Impact factor: 4.379

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