The remotely controlled living robot by ETH Zurich Motivation: - - PowerPoint PPT Presentation

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the remotely controlled living robot by eth zurich
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The remotely controlled living robot by ETH Zurich Motivation: - - PowerPoint PPT Presentation

Jul 20, 2023 169 likes •524 views

The remotely controlled living robot by ETH Zurich Motivation: Lemmings 2 Engineers First Draft 3 Information Processing Information Processing: ex vivo Cell Detection & Microscopy Controlling Cell Tracking Chemotaxis Movement

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SLIDE 1

The remotely controlled living robot by ETH Zurich

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SLIDE 2

Motivation: Lemmings

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SLIDE 3

Engineers’ First Draft

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SLIDE 4

Information Processing

Microscopy Cell Detection & Cell Tracking Controlling

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Movement Chemotaxis network Light switch Single E. lemming cell: in vivo + in silico Information Processing: ex vivo

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SLIDE 5

Bacterial Movement

Microscopy Cell Detection & Cell Tracking Controlling

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Chemotaxis network Light switch Information Processing: ex vivo Single E. lemming cell: in vivo + in silico Movement

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SLIDE 6

Bacterial Movement

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Directed movement (CCW) Tumbling (CW)

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Bias

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Small bias large tumbling frequency Large bias low tumbling frequency

Bias := probability of directed movement

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Modeling of Bacterial Movement

coordinates bias

directed movement tumbling transition probabilities

bias = 0.69 bias = 0.85 bias = 0.99

model calibration

from literature: movement behavior

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SLIDE 9

Chemotaxis Network

Microscopy Cell Detection & Cell Tracking Controlling

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Movement Light switch Information Processing: ex vivo Chemotaxis network

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CheY

CW Pi

CheZ periplasm cytoplasm CheR CheB

+CH3

  • CH3

Pi ATP ADP

CheA CheW MCPs CCW CW

Molecular Mechanism of Chemotaxis

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directed movement tumbling

flagellar motor

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SLIDE 11

Modeling of Chemotaxis Network

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4 different Chemotaxis network models implemented:

Model based on Che species Receptor species ODEs Parameters Extended Spiro et al. (1997) 6 12 18 30 Mello & Tu (2003) 6 15 21 24 Rao et al. (2004) 4 10 14 22 Barkai & Leibler (1997) 2 26 28 22

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SLIDE 12

Light switch

Microscopy Cell Detection & Cell Tracking Controlling

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Movement Chemotaxis network Information Processing: ex vivo Light switch Single E. lemming cell: in vivo + in silico

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Light switch: Two Approaches

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Pi Pi

Pi Pi

I: Archeal Light Receptor II: Che Protein Localization

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I: Archeal Light Receptor

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periplasm cytoplasm CCW directed movement CW tumbling

flagellar motor

CheZ CheR CheB

+CH3

  • CH3

Pi ATP ADP

CheA CheW

CW Pi

CheY

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SLIDE 15

I: Archeal Light Receptor

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Bba_K422002

0.04 0.08 0.12 0.16 0.2

OD at 500 nm (AU)

control with archeal light receptor

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SLIDE 16

CW Pi

CheZ periplasm cytoplasm CheR CheB

+CH3

  • CH3

Pi ATP ADP

CheA CheW

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CCW directed movement CW tumbling

flagellar motor

PhyB PIF3

CheY

PIF3

CheY

Anchor

II: Che Protein Localization

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SLIDE 17

Actin homologue MreB:

Cell Skeleton

Trigger factor TrigA:

Ribosome

Tet repressor TetR:

Plasmid DNA

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# 13,500 / cell # 8,000 / cell # 4,000 / cell

II: Che Protein Localization

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SLIDE 18

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BBF RFC 28: assembly of fusion proteins consisting of three parts in one step

Light sensor Linker Che Protein

AarI

cheY

5`CACCTGC TTTT GGAG GGGA AAAA CGTCCAC 3`

AarI

CCCT TTTT GCAGGTG 5` 3`GTGGACG AAAA CCTC

81 combinations!

II: Che Protein Localization

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SLIDE 19

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Modeling: Sensitivity Analysis

Anchor protein [µM] Anchor sites [µM]

Che protein Fusion Anchor AP

  • 1. CheY

CheY - PhyB 50 µM 40 µM

  • 2. CheR

trigA – Pif3

  • 3. CheB

Relative amplitude

II: Che Protein Localization

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Information Processing: ex vivo

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Movement Chemotaxis network Light switch Single E. lemming cell: in vivo + in silico Microscopy Cell Detection & Cell Tracking Controlling Information Processing: ex vivo

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Live Imaging of the E. lemming

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Microscopy

  • Main challenges:
  • Swimming out of

focus

  • Swimming out of

field

Cell Detection

  • Main challenges:
  • Fast for real-time

imaging

  • Good detection rate

Cell Tracking

  • Main challenges:
  • Fast for real-time

imaging

  • Robust
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Output image

In 0.2 seconds!

Input image

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Live Imaging of the E. lemming

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Controller

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Large bias: low tumbling frequency Small bias: large tumbling frequency

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Controller Competition

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5 Novel Controllers:

1. Threshold optimized controller Controller

  • E. Lemming

Imaging

System properties:

  • highly nonlinear
  • stochastic process
  • noisy
  • time delay

Cost function: Competition:

steer the E. lemming on a predefined path, while minimizing the deviation between reference and current direction Controlled system

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Closing the Loop: Results

Microscopy Cell Detection & Cell Tracking Controlling

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Movement Chemotaxis network Light switch Single E. lemming cell: in vivo + in silico Information Processing: ex vivo

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Closing the Loop: Simulation

  • E. coli
  • E. lemming

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Biological Implementation

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Angle over Time

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response time of the system adaptation directed movement

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Angular Speed over Time

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Speed over time

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Achievements

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The

  • E. lemming

BioBrick Toolbox MATLAB Toolbox

Closed information processing loop Lemming Game

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Acknowledgements

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Mario Marchisio Christoph Hold Vincent Rouilly Sven Panke Jörg Stelling

Special
friends:
Fabian
Rudolf,
Ralph
Streichan,
Nils
Goedecke,
Andreas
Meyer
and
 Christian
Femmer
and
the
E.
lemmings.


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SLIDE 33

Team

Thank you for your attention!

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Questions?

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