Life in the low-reynolds number world

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1 Lecture 11 Life in the low-reynolds number world Sources: Purcell Life at low Reynolds number (Am. J. Phys 1977) Nelson Biological Physics (CH.5) Tsvi Tlusty,

2 I. Friction in fluids. Outline II. Low Reynolds-number world. III. Biological applications. Viscous friction dominates mechanics in the nanoworld. Friction is dissipative: converts ordered motion into thermal energy. Implications of symmetry. Biological Q: Why don't bacteria swim like fish? Physical idea: motion in the nanoworld have different symmetry than motion in the macroworld.

3 I. Friction in fluids

Small particles can remain in suspension indefinitely Suspension of protein mwaterg mg z

net du dp j P D 0 (Smoluchowski's m net geq.

Example: Myoglobin: mg Vg m g Vg water Net force: m g Vg (Archimedes' principle) c z = c

4 Small particles can remain in suspension indefinitely Suspension of protein mwaterg mg z Gravity: Bouyancy force: water What happens after a long time? net du dp j P D 0 (Smoluchowski's m net geq. for eqilibrium) dx dx z B T m r net gz P( x) exp (Einstein's relation kbt D / ) kt k Example: Myoglobin: mg Vg m g Vg water Net force: m g Vg (Archimedes' principle) c z = c 0 e B 4 3 Myoglobin mass: m Da =.710 kg 0 net mass: mnet m/ kg scale height z kt B * 0 mnet g 60 m Density in test-tube is ~ constant.

5 Centrifuges can achieve a much higher g ω fcentrifugal mnet r m Centripetal acceleration is by frictional drag: du jv P f P( r) mnet P( r) r dr Balanced by diffusion current dp() r jd D dr r dp j jv jd 0 mnet P( r) r D 0 dr m Pr ( ) exp r net kt B How long does it take to reach equilibrium?

6 Sedimentation time scale depends on solvent viscosity Sedimentation velocity (depends g not intrinsic property) v m g drift net mnet g Sedimentation time scale: v g drift mnet mnet Unit is Svedberg (10-13 sec) The sedimentation scale is determined by the size and mass of the particles and the viscosity of the surrounding fluid. For a sphere 6 R where is the viscosity The viscosity of water at room temperature is Pa s = 10 poise (erg/cm s)

7 Rheology is useful to study macromolecules Example: polymer size scaling. Assuming random walk Rg m net ~ m p m Random walk: p 0.5 Self-avoiding: p 0.57 D kbt kbt 6R g ~ m p s m m m net net ~ p 6Rg m m 1 p D ~ 0.57 m s ~ 0.44 m

8 Experiment: ink in glycerin Hard to mix a viscous liquid The clockwise-counterclockwise experiment: blob will smear out but retracing make the blob reassemble into nearly original position and shape! That's not what happens when you stir cream into your coffee

9 Does reversibility violates nd law of TD? Ink diffuses but very slowly: kbt kbt D So the blob cannot change much by diffusion D 0. Stirring causes organized motion: fluid layers slide over one another. Ink molecules spread out but not randomly (because diffusion is too slow). Reversing the wall motion: fluid layers slide back and reassemble the blob. Such organized flow is called laminar.

10 In RGB

11 II. Low Reynolds-number world Quantifying the friction-dominated regime (laminar vs. turbulent)

Forces in laminar flow f A v L Shear motion: moving plate feels resisting viscous force stationary plate feels opposite force (entraining force).

12 Forces in laminar flow f A v L Shear motion: moving plate feels resisting viscous force stationary plate feels opposite force (entraining force). Viscous force f is proportional to area A, and speed v but decrease with plate separation. Empirically, for small v, many fluids follow simple law:

13 Newtonian fluid z y x vy ( ) f dxdz v dv v y dy y Uniform flow along x Force applied on y+dy layer by y layer f dv dy (Newtonian viscous formula) Coefficient of viscosity

14 Critical force demarcates the friction-dominated regime Intuitively, flow is laminar when viscosity η is large and turbulent if η is small. But small or large w.r.t. what? Dimensional analysis for Newtonian fluid: force M [ ] ; [ ] velocity x length LT M 3 L No dimensionless quantity from η and ρ. But we can make a characteristic quantity. f crit critical viscous force no intrinsic length scale: cannot tell thick from thin fluids. Newtonian fluid is scale invariant. Situation dependent: fluid motion is viscous if f f crit.

15 Aquatic cellular environment is viscous For macroscopic bodies and forces water is turbulent. For pn forces in the cell, water is viscous For f < f crit, fluid is thick: friction quickly damps out inertial effects. Flow is dominated by friction.

dx Net force on fluid: f f ( x l) f ( x ) 0 0 df d v 3 v f friction f ~ l Al l dx dx R Reynolds number 3 finertia l v / R vr 3 friction l v / R f Small

16 The Reynolds number quantifies the relative importance of friction and inertia Flow past a sphere: Velocity changes direction during t ~ R / v. Acceleration magnitude ~ / ~ / a v t v R Newton's law f f f ma ( f is by fluid pressure) ext ext frict tot 3 v finertia = ma l R f dv friction force: A dx Net force on fluid: f f ( x l) f ( x ) 0 0 df d v 3 v f friction f ~ l Al l dx dx R Reynolds number 3 finertia l v / R vr 3 friction l v / R f Small Re: friction dominates; flow stops immediately when force stops ("creeping flow ). Big Re: inertial effects dominate, coffee keeps swirling; flow is turbulent.

3 3 10 kg m 30 m10 m/s 3 10 Pa s Microbiology is viscous

17 kg m 30 m10 m/s 3 10 Pa s Microbiology is viscous (low Re) kg m 10 m3010 m/s 3 10 Pa s

18 Tuning Re Australian Pitch drop experiment running from 197 Viscosity ~ 10 1 of water

x, y, z x v0t, y, z d x x v : x v t, y, z x v t d d 0 0 0 x v0 d t, y, z x, y, z friction force: f A dv dx Once the top

19 Time-reversal properties of a dynamical law signal its dissipative character Sheets move uniformly dv x const. v v dx d 0 forces balance out: Time depndent motion: x v( x, t) v0( t) d f f f crit inertia negligible Unmixing: x v0 : x, y, z x v0t, y, z d x x v : x v t, y, z x v t d d x v0 d t, y, z x, y, z friction force: f A dv dx Once the top plate has returned to its initial position, each fluid element has also returned, regardless of the dynamics of the return stroke.

20 Time reversal: Newtonian mechanics dz dt dz du m f mg dt dz g solution 1 z() t v0t gt In Newtonian physics, the timereversed process is a solution to the equations of motion with the same sign of force as the original motion. Time reversal: t t dz dt g solution z() t vt 0 1 gt Time-reversed trajectory solves Newton's law with inverse v 0.

21 Time reversal: Diffusion dc dt D d c dx solution 1 c( x, t) exp 4Dt x 4Dt Time reversal: t t dc dt dc D d x solution 1 c( x, t) exp i 4Dt x 4Dt Diffusion equation is not time invariant. Time-reversed solution does not solve original diffusion equation.

22 Viscous friction is not time reversal invariant A ball in highly viscous fluid f dz dt f solution: f z z0 t Time-reversed solution does not solve original friction equation, f dz dt f solution: f z z0 t unless force is inversed Frictional motion is irreversible because friction dissipates ordered motion into heat.?

23 Fluids and solids differ in time-reversal symmetry (displacement) f A G du dy y u No explicit time dependence: invariant. x Solids have memory of position. f d du A dy dt y v Not invariant. x

24 Fluids and solids differ in time-reversal symmetry m du dt ku f ku k nd order time derivative: invariant. Solids have memory of position. du dt f f 1 st order time derivative: Not invariant. 6 R

Viscous flow have other symmetry properties Stokes flow: p v The reversed flow with v v p p obeys the same equation. Low Re flow around a stationary object having a plane of symmetry is symmetric.

25 Viscous flow have other symmetry properties Stokes flow: p v The reversed flow with v v p p obeys the same equation. Low Re flow around a stationary object having a plane of symmetry is symmetric. Proof: Symmetry plane x 0. Flow reversal: v( x, y, z) v( x, y, z). Mirror symmetry: v ( x, y, z) v ( x, y, z) v ( x, y, z) x x x v ( x, y, z) v ( x, y, z) v ( x, y, z) y, z y, z y, z Sensitive test for small Re flows

26 upon reversal, fluid follows the identical streamlines in the opposite direction. Stokes flow: p v In low Re we can blow out a candle either by blowing or suction. In high Re, we cannot blow out a candle by suction

27 Streamlines are invariant to rate of flow Stokes flow: p v ( p) ( v) Follows form linearity of the flow. No notion of explicit time. v ( r, t) and v ( r, t) solutions 1 v with v 1 1 is also a solution p p p 1 1

28 III. Biological applications

29 Swimming and pumping In the low Re world: a motion can be canceled completely by applying minus the timereversed force. What are the implications for microorganisms? Flapping back and forth returns every fluid element to its original position: No net motion!

30 Swimming of microorganisms: reciprocal motion a. paddles move backward at speed v relative to the body forward motion of the body at speed u relative to water. b. paddles move forward at v' relative to the body backward motion of body at u' relative to water. c. Repeat Any net motion? [Cartoon by Jun Zhang.]

31 relative velocity of paddles w.r.t. fluid: vu drage force on paddles: f ( v u) paddle p drag force on body: f b u b force balance: f p f b body velocity: u v b p p Total displacement: x ut vt b p p

32 paddle Similarly: relative velocity of paddles w.r.t. fluid: ' ' drage force on paddles: ( ' ') drag force on body: body velocity: Total displacement: p b b p b p v u f v u f u u v x u p b p t v t

33 In reciprocal motion the paddles return to their original position: vt v t Hence: p p x u t v t vt ut x b p b p NO NET MOTION!

34 Scallop theorem forbids strictly reciprocal motion Scallop theorem: Strictly reciprocating motion won t work for swimming in the low- Reynolds world [Purcell (1977) Am. J. Phys.] What other options a microorganism has? Motion must be periodic (to be repeated). It can t be of the reciprocal.

35 Ciliary propulsion is periodic not reciprocal Many cells use cilia to generate net thrust. Each cilium contains internal filaments and motors. Cilia can be used for translocation and pumping (in stationary cells). The difference is in the additional degrees of freedom.

36 Net motion requires breaking the back and forth symmetry Large drag in forward motion. Displacement: p vt x ut vt 1 / b p b p Smaller drag in backward motion: p p Displacement: p vt x ut vt 1 / b p b p Total displacement: b p p vt v t x x vt 1 / 1 / b p b p b p b p 0

37 Cilia break symmetry by changing the direction of motion Effective stroke: high drag (perpendicular) Recovery stroke: low drag (parallel)

38 Bacteria use rotating flagella for locomotion

39 Flagella break shape symmetry for locomotion f f =-ζ v f =-ζ v v v v f f f v v f not parallel to v The drag coefficients parallel and perpendicular to the cylinder (helix) are not equal. Although the velocity is in y-x plane, there is a z-component of the force. The net force on the helix is in z direction.

40 How bacteria avoid rotating by torque? Bacteria are large enough such that friction slows down rotation Bacteria may also have pairs of flagella rotating in opposite directions.

41 Two coupled scallops can move Single pair of paddles Dimer of pairs of paddles Strictly reciprocal No net motion Single pair: strictly reciprocal Dimer: nonreciprocal Net motion! [Lauga and Bartolo (008) PRE]

Why should bacteria move and stir? Eating? It s anyhow hard to mix: Streamlines around Volvox (protozoa) -- Only a few streamlines reach a moving object. Solution: use diffusion. Why stir?

42 Why should bacteria move and stir? Eating? It s anyhow hard to mix: Streamlines around Volvox (protozoa) -- Only a few streamlines reach a moving object. Solution: use diffusion. Why stir? -- Cilia of length d refreshes its volume every t stir = d/v -- diffusion time scale is t diff = d /D Only if t stir < t diff this is worthwhile. Peclet number: For D = 1000 μm /s and d =1 μm, v = 1000 μm/s Pe t diffusion t stir dv D Bacteria swim for other reasons, like food gradient

43 Vesicular delivery networks are essential for macroscopic organisms that cannot rely on diffusion R Constraints: vr ( ) 0 (non-slip) v(0) v kg/m ; R10 m 3 10 cm/s ; =10 Pa s vr (within low Re) 3 10

44 Balancing the forces: R Pressure applies force: df rdr p Viscous force from inner shell pushes shell forward: dv() r dfin rl ( dv / dr 0) dr r p Viscous force from outer shell pulls shell backward: dv( r) dv( r) d v( r) dfout r dr L r dr L dr dr rdr dr r dr r df df df df p in out dv d v r pdr L dr rl r dr 0 dr dr df p 1 dv d v 0 0 L r dr dr

45 Poiseuille flow: R df p 1 dv d v 0 0 L r dr dr Flux Q R 0 rdrv( r) 8L 4 R p General solution: p v( r) A B ln r r 4L Boundary conditions: p v() r R r 4L The flow is laminar in most blood vessels in the human body except for the largest veins and arteries. Q ~ R 4 flow can be controlled by small variation of radius.

46 Viscous force at DNA replication fork Since the two single strands cannot pass through each other, the original must continually rotate. Would frictional force resisting this rotation be enormous? R ω Y-shaped junction

10.5 bp/turn 1000 600 rad/s 10.5 W L k T m 1 3 ( )(600 s )(10 Pa s)(1 nm ) ~ 0.

47 Viscous force at DNA replication fork The torque scales like: r f RRL R The dissipation work P R L per turn of : W R L ω Replication rate: 1000 bp/s DNA period: 10.5 bp/turn rad/s 10.5 W L k T m 1 3 ( )(600 s )(10 Pa s)(1 nm ) ~ 0.01 L B / Small friction compared to energy consumed by DNA helicase which unzips DNA. Y-shaped junction

48 Summary

49 Viscosity dominates the nano-world. Suspension is stabilized by diffusion at time scale: v g drift mnet mnet Hard to mix viscous fluids Reynolds number: Inertia/friction Force/critical force Reynolds number 3 finertia l v / R vr 3 friction l v / R f Symmetry: Newtonian dynamics: time-reversal invariant Viscous friction: not time-reversal invariant Swimming of microorganisms: Strictly reciprocal motion cannot translocate Periodic but not reciprocal motion work in ciliary and flagellar propulsion Viscosity dominates flow in blood vessels.

Lecture 12. Life in the low Reynolds-number world

Lecture 12. Life in the low Reynolds-number world Zhanchun Tu ( 涂展春 ) Department of Physics, BNU Email: tuzc@bnu.edu.cn Homepage: www.tuzc.org Main contents Friction in fluids Low Reynolds-number world