title: Mechanical catalysis on the centimetre scale.
abstract: Enzymes play important roles in catalysing biochemical transaction paths, acting as logical machines through the morphology of the processes. A key challenge in elucidating the nature of these systems, and for engineering manufacturing methods inspired by biochemical reactions, is to attain a comprehensive understanding of the stereochemical ground rules of enzymatic reactions. Here, we present a model of catalysis that can be performed magnetically by centimetre-sized passive floating units. The designed system, which is equipped with permanent magnets only, passively obeys the local causalities imposed by magnetic interactions, albeit it shows a spatial behaviour and an energy profile analogous to those of biochemical enzymes. In this process, the enzyme units trigger physical conformation changes of the target by levelling out the magnetic potential barrier (activation potential) to a funnel type and, thus, induce cascading conformation changes of the targeted substrate units reacting in parallel. The inhibitor units, conversely, suppress such changes by increasing the potential. Because the model is purely mechanical and established on a physics basis in the absence of turbulence, each performance can be explained by the morphology of the unit, extending the definition of catalysis to systems of alternative scales.
authors: Department of Informatics, University of Zurich, Andreasstrasse 15, 8050 Zurich, Switzerland Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar St., Cambridge, MA 02139, USA shuheim@csail.mit.edu.
authors: Shuhei
authors: S
authors: Miyashita
authors: Department of Informatics, University of Zurich, Andreasstrasse 15, 8050 Zurich, Switzerland Department of Bioinformatics, University of Wurzburg, Biocenter, Am Hubland, 97074 Wurzburg, Germany.
authors: Christof
authors: C
authors: Audretsch
authors: Department of Architecture, ETH Zurich, John-von-Neumann-Weg 9, 8093 Zurich, Switzerland.
authors: Zoltán
authors: Z
authors: Nagy
authors: Institute of Applied Mathematics and Physics, Zurich University of Applied Sciences, Technikumstrasse 9, 8400 Winterthur, Switzerland European Centre For Living Technology, S. Marco 2847, 30124 Venezia, Italy.
authors: Rudolf M
authors: RM
authors: Füchslin
authors: Department of Informatics, University of Zurich, Andreasstrasse 15, 8050 Zurich, Switzerland Institute of Academic Initiatives, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan Department of Automation, Shanghai Jiao Tong University, 800 Dong Chuan Rd, Min Hang, Shanghai 200240, China.
authors: Rolf
authors: R
authors: Pfeifer
mesh_terms: D001671:Biochemistry / Q000379:methods*; D001703:Biophysics / Q000379:methods*; D002384:Catalysis; D003198:Computer Simulation; D004798:Enzymes / Q000502:physiology*; D007700:Kinetics; D008280:Magnetics; D008956:Models, Chemical; D009038:Motion; D066330:Printing, Three-Dimensional; D011487:Protein Conformation; D012984:Software; D013269:Stochastic Processes; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D004798:Enzymes; D014867:Water
keywords: autocatalysis; conformation change; enzyme; inhibitor; magnetic catalysis; reaction phase
references: Science. 2000 Aug 18;289(5482):1170-2
references: 10947979
references: Nat Mater. 2003 Apr;2(4):241-5
references: 12690397
references: Science. 2002 Mar 29;295(5564):2418-21
references: 11923529
references: Proc Natl Acad Sci U S A. 2000 Feb 1;97(3):984-9
references: 10655471
references: Artif Life. 2012 Spring;18(2):129-42
references: 22356155
references: Science. 2002 Apr 12;296(5566):323-5
references: 11951039
references: Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9580-4
references: 17522257
references: Science. 1997 Apr 11;276(5310):233-5
references: 9092466
references: Angew Chem Int Ed Engl. 2003 Jul 28;42(29):3368-71
references: 12888960
references: Langmuir. 2010 Aug 3;26(15):12534-9
references: 20597527
references: Nature. 2000 Jun 29;405(6790):1033-6
references: 10890439
references: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):4937-40
references: 11959945
references: Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Aug;68(2 Pt 2):026207
references: 14525084
references: Science. 2004 Jan 16;303(5656):348-51
references: 14726585
references: J Am Chem Soc. 2002 Dec 11;124(49):14508-9
references: 12465940