Elastic knots

(elastic beam under nite rotation and self-contact) Sbastien Neukirch CNRS & Univ Paris 6 (France) dAlembert Institute for Mechanics
joint work with:

Nicolas Clauvelin (PhD work) Basile Audoly

Tensile strength of a wire

shing line

10 kg

Stasiak et al, Science (1999)

Tensile strength of a wire

shing line with knot

6 kg

Stasiak et al, Science (1999)

Knots are everywhere

Long enough polymers are (almost) certainly knotted
Sumners+Whittington, J. Phys. A : Math. Gen. 1988

273 knotted proteins in the ProteinDataBank (1%) Single molecule experiment with knotted F-Actin laments
Arai et al, Nature (1999)

Ab-initio molecular simulations for alcane molecule (C10H22)

Saitta et al, Nature (1999)

Elastic knots
T self-contact T

h
- Length L - Circular cross-section: radius h - Bending rigidity : E I - Twist rigidity : G J
E :Youngs modulus G : shear modulus
5

h4 I= 4 h J= 2
4

Elastic laments
climbing plants

Theory F M
Applications

S=0

DNA supercoiling

cables brous proteins

Kirchhoff equations

apply to : - slender bodies - not too bent

7

Kirchhoff equations

M F

Kirchhoff equations

s
M

M F

Kirchhoff equations

s
M

M F

10

Kirchhoff equations
r(s+ds)

r(s)

s+ds

11

Kirchhoff equations
p(s) ds r(s) -F(s) r(s+ds)

s+ds

F(s+ds)

12

Kirchhoff equations
p(s) ds r(s) -F(s) r(s+ds)

s
Equilibrium

s+ds
F(s+ds) - F(s) +p(s) ds =0 F(s) + p(s) =0
13

F(s+ds)

Kirchhoff equations
p(s) ds r(s) -F(s) r(s+ds) M(s+ds)

M(s) Equilibrium

s
M + r x F =0
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s+ds

F(s+ds)

Kirchhoff equations
e x d 2 d d d 1 d 2 3

Cosserat frame

d1 = u d1 d2 = u d2 d3 = u d3
u = {1 , 2 , }di
curvatures twist

y
15

Kirchhoff equations
constitutive relations curvature
M d1 = EI 1 M d2 = EI 2 E I

Youngs modulus second moment of area

twist
M d3 = GJ
16

G J

shear modulus polar moment of area

Kir chhoff equations

21 ODEs with variable : s
ordinary differential equations

boundary conditions - how the rod is held - few solutions are admissibles
D1=0 A1 A2

21 unknowns

d ! F $! p ds d ! ! ! M $F &d 3 ds d r $! ! d3 ds d ! d i $u & !i ! d ds m i $K i ui
linear elasticity

! " s# F ! " s# M r " s# ! ! " s# d3 ! " s# d2 ! " s# d1 3 u " s# !

D2 A1

A2

l
D3 A2 A1

i$1,2 ,3

r " A2 #%r " A1 #$k ! " A2 # d3 ! ! " D$L%k #

17

! " A1 #$! " A2 # d3 d3

Boundary value problem

Y S=-L/2 S=L/2 D X Z S=0
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(T ,M )

Boundary value problem

3 contact points Y

s1

s2

s3
X

S=L/2

symmetries : X => - X Y => Y Z => - Z

Z S=0 - Shooting method (Mathematica) - Gauss colocation (AUTO)

20

Numerical Path Following : Results

T L2 t= (2)2 EI

Planar Elastica

t=

2/ d

D d= L

Distance of self-approach
sb
(sa , sb )
(sa , sb ) 2h

sa
S=0

sa

(sa , sb ) < 2h
22

sb

Distance of self-approach
sb
(sa , sb )
(sa , sb ) 2h

sa
S=0

sa

(sa , sb ) < 2h
23

sb

Making the rod thinner

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Making the rod thinner

25

Making the rod thinner

26

Making the rod thinner

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Making the rod thinner

28

Making the rod thinner

29

Making the rod thinner

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Zero thickness limit

singular point

EI equilibrium : T = 2 2R

Arai et al (1999)

tensile force T

singular point

EI bending moment R
31

P2

Total contact force

s3
T

s1
P1

s2
P3

h
S=0
1 T 1 T Pi
i

1/2

Pi
i

0.55 (h/s2 )

1/2

h/s2

Kirchhoff Equations
F M t R = p

= F t 1 = M t EI = t

forces equil. moments equil. kinematics tangent def.

d ds
p(s) ext. pressure F (s) internal force
M (s) internal moment R(s) position
33

t(s) tangent

Planar Elastica

s T EI = T sin

(s) T

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Planar Elastica
large T
T T

EI = sin T

singular perturbation
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Planar Elastica
large T
T T

EI = sin T

sin 0 (s) 0

singular perturbation
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Planar Elastica
large T
T T

EI = sin T

sin 0 (s) 0

(s) rapidly varying

region size : inner layer
37

singular perturbation

EI T

Perturbative problem
=0 (h = 0)

small parameter
= 2h T EI
2 1/4

h
38

Matched asymptotic expansions

braid
tail tail

loop

small parameter :

2h T EI
2
39

1/4

Braid : self-contact zone

braid
tail tail

loop

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Braid : linear superposition

1

small deections => linear problem

x , x
A B

x +x
B

=
twice more rigid 1 1 curvature: 2 R
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x x

self-contact => contact with obstacle

Kirchhoff Equations
F M t R = F t 1 = M t EI = t = p

forces equil. moments equil. kinematics tangent def.

d ds
p(s) ext. pressure F (s) internal force

constitutive relations: curvature M = EI M = GJ twist

M (s) internal moment R(s) position
42

t(s) tangent

Braid : boundary value problem (BVP)

u () v () u () v () = = = = 0 +1 0 0
unit radius

v
u v = 0 = 0

u z

xB xA u= 2 yB yA v= 2

boundary conditions

u () + v () = 1
2 2

u v

= =

2 p() u() 2 p() v()

u v

= 0 = 0

p() =?

moments forces

u (+) v (+) u (+) v (+)

= = = =

0 1 0 0

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boundary conditions

Braid : rst kind of solutions

u () + v () = 1
2 2

v u z

unit radius

boundary conditions

u (1 ) = 0 u (1 ) = 0 v (1 ) = 0 v (1 ) = 1

u v

= =

2 p() u() 2 p() v()

= =

u = cos(()) v = sin(())
2

6 2 3
4

p()

/ 2

(0) = 0 (0) = 0.54 (0) = 0 (0) = 0.004 1 = 3.50

Braid : second kind of solutions

P1 P2 P3

v u z
boundary conditions

3
unit radius

u (+3 ) = 0 u (+3 ) = 0 v (+3 ) = 0 v (+3 ) = 1

u v

= =

2 p() u() 2 p() v()

avec
u

p() = P1 ( 1 ) + P2 ( 2 ) + P3 ( 3 )

u(0) = 1 u (0) = 0 u (0) = 0.25 v(0) = 0 v (0) = 0.76 v (0) = 0 v (0) = 0.38 u (0) = 0.66

3 = 1 = 2.66 ; 2 = 0 ; P1 = P3 = 0.32 ; P2 = 0.35

Braid : third kind of solutions

P2 P1 P1 P2

v u z
boundary conditions

2 1 1
=0

2
unit radius

u (+2 ) v (+2 ) u (+2 ) v (+2 )

= = = =

0 1 0 0

1 2 P1 P2

= 0.35 = 2.68 = 0.12 = 0.31

Braid : contact topology

side view
1.0 0.5 - 2.0 - 1.5 - 1.0 - 0.5 - 0.5 - 1.0
47
1.05 1.04 1.03

inter-strand distance

0.5

1.0

1.5

1.02 1.01 1.00 0.99 -3 -2 -1 0 1 2 3

Braid : contact topology

Braid : contact topology

Results
T
R R= EI 2T
1/2

p(s)

h
(EI)
1/4

= 9.91 h

1/4

Contact pressure p(s) Total contact force P =

0
50

p(s)ds = 0.82 h

1/2

(EI)

1/4

3/4

Experiments

Tong et al., Nature 2003

R=

EI 2T

silica wire h = 1/2 micron

Experiments

h R
52

h/R0

Fin

Braid : variational formulation

Kirchhoff equations => minimizing an energy

1 V = 2
+

+v

d + v (+) + v ()

with constraint:
u2 () + v 2 () 1 ,
54

}
work of external applied moments

Twist Instability

numerical simulations : M. Bergou, M. Wardetzky, S. Robinson, B. Audoly, and E. Grinspun. ACM Transactions on Graphics (SIGGRAPH), 2008

55

Twisted rods : the ideal case

if rod is uniform, isotropic, naturally straight system reduction 21 D => 6D
r d3 = d3 = (F r + M0 ) d3

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