Materials Science Division Argonne National Laboratory … · 2015. 11. 9. · Materials Science...
Transcript of Materials Science Division Argonne National Laboratory … · 2015. 11. 9. · Materials Science...
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Collective Motion in Active Systems
Igor Aronson Materials Science Division
Argonne National Laboratory
Department of Applied Mathematics and Engineering Sciences, Northwestern
University
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Outline of the course • Overview of experiments • Complex Ginzburg-Landau model and pattern-forming
instabilities • Self-organization of active polar rods: application in vitro
cytoskeletal networks • Collective motion of interacting self-propelled particles
• Lectures • Purpose: to teach a variety of research tools
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Outline of the course • Overview of experiments • Self-organization of active polar rods: application in vitro
cytoskeletal networks • Collective motion of interacting self-propelled particles
• Purpose: to teach a variety of research tools at the interface
of mathematics, physics and biology
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• Introduction
• patterns in granular systems
• in vitro cytoskeletal networks • suspensions of swimmers
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Where in the World is Argonne?
• World-Class Science • Unique Scientific Facilities • Free and Abundant Parking • 25 min from Downtown Chicago • White Deer (almost extinct)
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Argonne National Laboratory
• Argonne is a multidisciplinary science and engineering research center
• Mission: address vital national challenges in clean energy, environment, technology and national security.
• Total 3,350 employees, 1250 scientists • Budget: $800 million • 15 research division, 6 national user facilities
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World-Class User Facilities advanced photon source center for nanoscale materials
leadership computing facility electron microscopy center
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Materials Science Division www.msd.anl.gov • design, synthesis, fabrication, and characterization of
advanced materials for energy production, distribution, storage, and efficiency
• broad spectrum of research, from superconductivity, magnetism to biological materials
• staff: senior scientists – 20, scientists – 25, junior scientists-8, postdocs – 40-50, students – 30
• budget: $35 million • Papers published per year: > 300 (large fraction in high-
profile journals – Nature, PRL, PNAS etc )
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Definition of Soft Matter • Soft Matter - a subfield of condensed matter
dealing with physical states that are easily deformable by thermal fluctuations and external stresses.
• Examples: complex liquids, colloids, gels, polymers, biological materials
• Simple introduction: I Aranson, Collective Behavior in Out-of-Equilibrium Colloidal Suspensions, Comptes Rendus Physique, v14, 518 (2013)
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Active Matter • Active Matter - new field of condensed matter physics focused on
the physical and statistical properties of a wide class of systems actively consuming energy from environment, such as assemblages of active self-propelled particles. The particles have a propensity to convert energy stored in the medium to motion.
• Examples: suspensions of swimming bacteria and synthetic microswimmers, cytoskeletal networks, school of fish etc
• Simple introduction: S. Ramaswamy, The mechanics and statistics of active matter. Ann Rev Condens Matter Phys 1(1):323–345 (2010) T. Vicsek, A Zafeiris, Collective Motion, Physics Reports, v517, 71, 2012
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Dynamic Self-Assembly • SA-naturaltendencyofsimplebuildingblockstoorganize
intocomplexfunc:onalarchitectures,frombiomoleculestolivingcells
• uniqueopportunityformaterialsscience–alterna:vetolithography
• self-assembledmaterialsareintrinsicallycomplex,withahierarchicalorganiza:onovernestedlengthand:mescales
• sta:c(equilibrium)vsdynamic(ac:ve)self-assembly• ac:ve(outofequilibrium)assembledemergingstructures
arenotaccessibleunderequilibriumcondi:ons
Introduc*on:G.M.Whi*sides,BGrzybowski,Self-Assemblyatallscales,Science,v295,2418(2002)
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Collective Behavior in Living and Synthetic Matter
swarming hungry locusts
Sumino et al, Nature 2012 I. Cousin et al, Science, 2005
• simple interactions – complex emergent behavior • different mechanisms – similar patterns • no obvious leader
swirling microtubules
Blair, Kudrolli, 2003
swirling granular rods
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Seemingly Intelligent behavior • no obvious leader • only local interactions between the individuals
Myxobacteria Starlings (birds)
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Opposite is also true! • Highly intelligent beings (humans) - simple behavior
humans in square room bottleneck
Karamouzas, Skinner, Guy, Universal Law Governing Pedestrian Interactions, Phys Rev Lett, 2014
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1. Polar orienting interaction in a noisy environment
2. Streaming: motion along the polar direction
• More complicated continuum hydrodynamic models (Tu, Toner, Ramaswamy)
Vicsek Model: A Major Theoretical Milestone • Point particles (boids - birdoids) move off-lattice
• Driven overdamped (no inertia effects) dynamics
• Strictly local interaction range
• Alignment according to average direction of the neighbors
• Simple update algorithm for the position/orientation of particles • Not necessarily reproduce observed phenomenology • Only two parameters – radius of interaction and noise magnitude
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Simulations of Vicsek model
Chate and Gregoire,PRL 2004
1,000,000 boids Fish school
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Simulations of Vicsek model: Phase transition
at large size, discontinuous transition
Order parameter: Magnitude of average velocity (similar to magnetization)
( ) ∑=
=N
ii tvN
t1
)(1ϕ
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Fundamental issues we will investigate
• Similarity between collective behaviors in living and inanimate systems
• Role of long-range interactions vs short-range collisions • Derivation of mathematical models from simple interaction
rules
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Active Systems are Complex
• Focus on simple yet non-trivial systems such as in vitro cytoskeletal networks, bacterial suspensions, swimmers
• Fundamental interactions are simple and well-characterized
• Interactions are mostly of the “physical nature”: inelastic
collisions, self-propulsion, hydrodynamic entrainment, vs chemotaxis, visual signaling, intelligence, etc
• Derive continuum description from elementary
interaction roles and connect observed patterns with experiment
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Multi-Scale Approach • Microscopic discrete models (self-propelled particles –
Vicsek model)
• Mesoscale probabilistic Boltzmann/Fokker-Plank equations
• Continuum microscopic models (phenomenological
theory by Toner and Tu, Ramaswamy) or derived from the Boltzmann equation (Boltzmann-Ginzburg-Landau Approach)
• Purpose: bridge 3 levels of description
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Understanding, controlling, and building complex hierarchical structures by • mimicking nature’s self- and directed-assembly
approaches
• design and synthesis of environmentally adaptive, self-healing materials and systems
http://science.energy.gov/bes/mse/research-areas/biomolecular-materials/
Active Matter and grand challenges in materials science
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Active Self-Assembled Systems – A Unique Opportunity for Materials Science
• Design of active self-assembled structures with functionality not available under equilibrium conditions
self-assembled colloidal robot neutrophil chasing a bacterium Snezhko & I Aranson, Nature Materials, 2011
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Survey of experimental systems
• Granular materials: vibration, friction, collisions
• Cytoskeletal networks: molecular motors, collisions, chemical interactions
• Suspensions of swimmers such as bacteria: rotation of flagella, hydrodynamic interactions, collisions
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Blair-Neicu-Kudrolli experiment
0 sin( )tωΓ = Γ
long Cu cylinders # of particles 104 6.2 mm
0.5 mm
vibration of long rods top view
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Phase transitions and vortices
• Weakly vibrated layer of rods
• Phase transition
• Coarsening
• Vortex motion
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Long-Term Evolution
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Origin of Motion Experiment Simulations
D Volfson, L Tsimring, A. Kudrolli , Phys Rev E (2004)
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Swarming in Quasi-2D Experiments Experiment, 500 asymmetric rods Simulations, 500 rods
Lumay, D Volfson, L Tsimring, A. Kudrolli PRL 2008
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Vibrated Polar Disks Experiment, 1000 asymmetric disks
re-injecting boundary conditions (multi-petal dish)
Deseigne, Dauchot, Chate, PRL 2010
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nanofabrication: micron-size AuPt rods swim in H2O2
AuPt & AuRu microrods are provided by Ayusman Sen and Tom Mallouk, PSU
Movie: Argonne
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Cytoskeleton - components
• Actin (red)
• Microtubules (MTs, green) • (1-20 mm, d=24 nm, rigid)
• Motors ( polarity)
• Crosslinks
(1-20 µm, d=8 nm, semiflexible)
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Molecular Motors Kinesin motor converts ATP to ADP
and perform mechanical work
Functions: muscle contraction, cargo transport, cytoskeleton organization, cell division
microtubules
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In vitro: Actin-Myosin Motility Assay
V Schaller et al. Nature 467, 73-77 (2010)
Crowd surfing
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Moving Clusters and Swirls
V Schaller et al. Nature 467, 73-77 (2010)
moderate density higher density
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§ Simplified system with only few purified components § Experiments performed in 2D glass container: diameter
100 µm, height 5µm § Controlled tubulin/motor concentrations and fixed
temperature § MT have fixed length 5µm due to fixation by taxol
F. Nedelec, T. Surrey, A. Maggs, S. Leibler, Self-Organization of Microtubules and Motors, Nature, 389 (1997) T. Surray, F. Nedelec, S. Leibler & E. Karsenti, Physical Properties Determining Self-Organization of Motors & Microtubules,
Science, 292 (2001)
in-vitro Self-Assembly of MT and MM
Cell with MT & MM
CCD camera
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Patterns in MM-MT mixtures Formation of asters, large kinesin concentration (scale 100 m)
100 µ
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Vortex – Aster Transitions
Ncd – gluththione-S-transferase-nonclaret disjunctional fusion protein Ncd walks in opposite direction to kinesin
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Dynamics of Aster/Vortex Formation
Kinesin Ncd
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Rotating Vortex Kinesin
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Summary of Experimental Results
• 2D mixture of MM & MT exhibits pattern formation • Kinesin: vortices for low density of MM and asters for
higher density • Ncd: only asters are observed for all MM densities • For very high MM density asters disappear and bundles are
formed
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New experiments: onset of spontaneous motion
• Short microtubules • Crowding agents • High concentration • Nematic ordering • Topologic defects
Sanchez et al, Nature, 2012
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Self-Propelled BioParticles • swimming aerobic bacteria Bacillus Subtilis • length 5 µm, speed 20 µm/sec, Re=10-4 • collective flows up to 100 µm/sec • need Oxygen (oxygentaxis)
5 µm
Turner, Ryu, and Berg (E. coli)
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Bacillus subtilis primary behaviors Collision of two bacteria in thin
films
Confining wall
Liquid
Concentration of bacteria near the surface due to gradient of dissolved Oxygen
Top
view
Side
vie
w
Ο2
Air
• Excellent swimmers • No tumbling
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Bacterial (or active) Turbulence Reynolds number 10-4
Dombrowski, Goldstein, Kessler, et al PRL 2004
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Schematics of Experimental Setup
Thin free-standing film concept Adjustable thickness
Adjustable concentration of bacteria
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pH-Taxis & concentration of cells
1sec 20sec 80sec
concentration vs. time Bacteria crowd control
pH indicator (bromothynol blue) was added field of view
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Bacterial Turbulence
Sokolov, Goldstein, Kessler, I.A PRL (2007)
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7-fold reduction of viscosity
• viscosity is extracted from the vortex decay time
• viscosity is extracted from the magnetic torque • viscosity vs concentration and swimming speed
of bacteria
vortex probe micro-rheometer Liquid film with
bacteria
Supporting frame
Magnetic deflecting system
Movable probe
Probe induced vortex
rotational micro-rheometer
Collective behavior
Magnetic coils
Nickel particle
Liquid film with bacteria
viscosity vs concentration
Sokolov & I.A, PRL 2009
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Novel Material Properties: Reduction of Viscosity
live bacteria dead bacteria
rotational rheology
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Mixing and self-diffusivity in bacterial suspensions Optical coherence tomography
Technical parameters
In-depth resolution = 15µm
Lateral resolution = 25µm
low coherence light source
photo detector
vertical scanning
reference mirror
beam splitter
deflecting system
3D concentration distribution
• collective swimming enhances mixing by a factor of 10
• confinement reduces mixing rates
• nontrivial 3D patterns result in enhanced transport
Sokolov, Feldstein, Goldstein, I.A, PRE 2009
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Machines Powered by Bacteria: Rectification of Chaotic Motion
Sokolov, Apodaca, Grzybowski, I.A, PNAS, December 2009
Size of gears: 350 µm, SU-8 photoresist Photolithography technique
Mass of Gear ~106 mass of bacteria
Collaboration with Bartosz Grzybowski,
Northwestern University 0.5 mm
Lithographic Mask
Featured in NY Times, Forbes, Wired, WDR, Sci American
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Gears Turned by Bacteria
1 mm
• 1-2 rotations per minute • Power about 1 femtowatt=10-15 Watt • About 300 bacteria power the gear
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Control of Rotation
• Rotation rate controlled by Oxygen/Nitrogen • Rotation rate depends on concentration
• Rotation enhanced by collective swimming
Rotation rate vs concentration
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Ratchet Mechanism of Rotation
• Bacteria slide along slanted edges • Trapped in junctions formed by the teeth • Simulations of Kaiser et al, PRL 2014
Trajectory of fluorescent tracers
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Expulsion of microswimmers by a vortical flow
Swimming bacteria Dead bacteria
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Bacteria follow director of the chromonic LC in a cell with strong planar anchoring
director
flat glass cell
Thickness h = 5-10 µm
Zhou, Sokolov, Lavrentovich, IA, PNAS 2014
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Zoom on individual bacterium
direct optical visualization of the 24 nm flagella!
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Tracer-bacterium interaction: cargo transport
Evidence for the long-range interaction
Sokolov, Zhou, Lavrentovich, IA PRE 2015
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Living LC in the biphasic domain higher temperature – nematic/isotropic phases co-exist
bacteria melt LC and nucleate tactoids – cloud chamber
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Collective Effects: Formation of Stripes scale depends on concentration, amount of oxygen
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Active Turbulence in LC