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Biological fluid mechanics at the micro‐ and nanoscale Lecture 7: Atomistic Modelling Classical Molecular Dynamics Simulations of Driven Systems Anne Tanguy University of Lyon (France). Atomistic Modelling : Classical Molecular Dynamics Simulations of Driven Systems. - PowerPoint PPT Presentation
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Biological fluid mechanics at themicro and nanoscale‐
Lecture 7:Atomistic Modelling
Classical Molecular Dynamics Simulations of Driven Systems
Anne TanguyUniversity of Lyon (France)
Atomistic Modelling:
Classical Molecular Dynamics Simulationsof Driven Systems.
I.Description II.The example of Wetting
III.The example of Shear Deformation
Classical Molecular Dynamics Simulations consists in solving the Newton’s equationsfor an assembly of particles interacting through an empirical potentiaL;
In the Microcanonical Ensemble (Isolated system): Total energy E=cst
In the Canonical Ensemble: Temperature T=cst
with if no external force
Different possible thermostats: Rescaling of velocities, Langevin-Andersen, Nosé-Hoover…more or less compatible with ensemble averages of statistical mechanics.
Equations of motion: the example of Verlet’s algorithm.
Adapt the equations of motion, to the chosen Thermostat for cst T.
• Langevin Thermostat:Random force (t)Friction force –.v(t) with <(t).(t’)>=cste.2kBT.(t-t’)
• Andersen Thermostat: prob. of collision t, Maxwell-Boltzman velocity distr.
• Nosé-Hoover Thermostat:
• Rescaling of velocities:
• Berendsen Thermostat: with
Heat transfer. Coupling to a heat bath.
after substracted the Center of Mass velocity, or the Average Velocity along Layers
0'dt
dH
( )1/2
)(. tFvdt
dvm ii
ii
Thermostats:
Examples of Empirical Interactions:
The Lennard-Jones Potential:
2-body interactions cf. van der Waals
Length scales ij ≈ 10 ÅMasses mi≈10-25 kgEnergy ij≈ 1 eV ≈ 2.10-19J ≈ kBTm
Time scale or
Time step t = 0.01≈ 10-14 s106 MD steps ≈ 10-8 s = 10 ns or 106x10-4=100% shear strain in quasi-static simulations
N=106 particles, Box size L=100 ≈ 0.1 m for a mass density =1.3.N.Nneig≈108 operations at each « time » step.
sm 12
2
10.
s
TD12
8
202
1010
10
)1(
1.0
The Stillinger-Weber Potential:For « Silicon » Si, with 3-body interactionsStillinger-Weber Potential F. Stillinger and T. A. Weber, Phys. Rev. B 31 (1985)
Melting T Vibration modes Structure Factor
The BKS Potential:For Silica SiO2, with long range effective Coulombian InteractionsB.W.H. Van Beest, G.J. Kramer and R.A. Van Santen, Phys. Rev. Lett. 64 (1990)
Ewald Summation of the long-range interactions, or Additional Screening (Kerrache 2005, Carré 2008)
OSijioùr
CeA
r
qqrE ijrB
ijji
BKSij ,),(
4)( 6
0
111 ).().(,,
)(4, ).()..(),...,2,1(
ararijkkji
arjiSW
ikijefeBrANE
2-body interactions(Cauchy Model) 3-body interactions
Example: Melting of a Stillinger-Weber glass, from T=0 to T=2.
Microscopic determination of different physical quantities:
-Density profile, pair distribution function
-Velocity profile
-Diffusion constant
-Stress tensor (Irwin-Kirkwood, Goldenberg-Goldhirsch)
-Shear viscosity (Kubo)
II. The example of Wetting
Surface Tension: coexistence beween the liquid and the gas at a given V.
(L. Joly, 2009)
The Molecular Theory of Capillarity:Intermolecular potential energy u(r).
Total force of attraction per unit area:
Work done to separate the surfaces:
(I. Israelachvili, J.S.Rowlinson and B.Widom)
Surface Tension:
h
h
h
zz
drruhrr
rfrddzhF
)()(.2
..
21
321
00
)(...2 321
hh
zS rurdrdhhFW
(Hautman and Klein, 1991)
3
.for cos. LVSLSVSLSVLV
III. The example of Shear Deformation
Boundary conditions:
Quasi-static shear at T=0.Fixed walls
Or biperiodic boundary conditions (Lees-Edwards)
Example: quasi-static deformation of a solid material at T=0°K
At each step, apply a small strain ≈ 10-4 on the boundary,And Relax the system to a local minimum of the Total Potential Energy V({ri}).Dissipation is assumed to be total during .
).10(10..
10/
418lim
12
LJusa
c
a
c
t
scat
Quasi-Static Limit
stressshear xyS
F
ux
Ly
y
xxy L
u
2strain
Rheological behaviour:
Stress-Strain curve in the quasi-static regime
stressshear xyS
F
ux
Ly
y
xxy L
u
2strain
X
y
Local Dynamics:
Global and Fluctuating Motion of Particles
stressshear xyS
F
ux
Ly
y
xxy L
u
2strain
Local Dynamics:
Global and Fluctuating Motion of Particles
Transition from Driven to Diffusive motiondue to Plasticity, at zero temperature.
cage effect (driven motion) Diffusive
y _
max
n ~ xy
p
Tanguy et al. (2006)
Driving at Finite Temperature:
The relative importance of Driving and of Temperature must be chosen carefully.
Low Temperature Simulations: Athermal Limit
Typical Relative displacement due to the external strain
larger than
Typical vibration of the atom due to thermal activation
ta ...
>>
h
B
k
Tk
Convergence to the quasi-static behaviour, in the athermal limit:At T=10-8 (rescaling of the transverse velocity vy et each step)
M. Tsamados(2010)
cste
.
4.0..
.
.
T= 0.2-0.5 Tg =0.435Rescaling of transverse velocities in parallel layers
Effect of aging
at finite T
Non-uniform Temperature Profile at Large Shear Rate
Time needed to dissipate heat created by applied shear across the whole system
Heat creation rate due to plastic deformation
Time needed to generate kBT,
LL
ctd
1
.
. xydt
dQ
.
. xy
BQ
Tkt
.
.
.
.
xy
BdQ
c
LTktt
Visco-Plastic Behaviour:
Flow due to an external force (cf. Poiseuille flow)F. Varnik (2008)
Non uniform T
End