Mesoscale Simulation Methods
Ronojoy Adhikari
The Institute of Mathematical Sciences
Chennai
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Outline
• What is mesoscale ?
• Mesoscale statics and dynamics through coarse-graining.
• Coarse-grained equations for a binary fluid-fluid mixture.
• Numerical methods of solution.
• Example simulations.
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Numbers and methods
1
2
3
4
5
6
7
0
Ab initio methods
Atomistic methods
Continuum methods
DFT
CPMD
MD
LD
BD
DPD
CFD
LB
Number of atoms (log) Simulation method Example of method
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How lengths scale with numbers
!! Try this for water
Molar mass = 18 gm
Molar volume = 18 mL
N = 1023
L 107˚
A
L N 1
3
N = 1
L 1˚
A
!! Are other scalings possible ? How does length grow with
size for a polymer ?
Throughout, (!!) indicate exercises/derivations/points to ponder.
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Length and time scales
pico
milli
micro
nano
nano micro milli
L
T
H = E
m ¨
R = ⇥U
˙
R = U
˙
c = D 2c
!! Are there systems with millimeter L but picosecond T ?
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How times scale with masses and lengths
m¨
x + kx = 0
2
0
= k
m
0
m
k
¨
u = c2 2u
0
= ±cq
⇥0 c
˙
u = D 2u
i 0
= Dq2
⇥0
2
D
Harmonic Oscillator Wave Equation Diffusion Equation
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Thermal fluctuations
P(x |x) =
1
⇤
2 D⇥
exp
(x x)2
2D⇥
⇥
Brownian motion : Einstein (1905)
D = kBT
6⇥ a
temperature
size
Stokes-Einstein-Sutherland Relation
Q. Why does a smaller particle have a higher
diffusion coefficient ?
A. The ‘root N’ effect! The central limit theorem
helps us understand this.
!! Is it (central limit) theorem or
central (limit theorem) ?
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Langevin theory
inertia
damping reversible force
fluctuation
deterministic stochastic
mean behaviour ‘root N’ fluctuations
regression to the mean
equilibrium fluctuations
v2⇥ = kBT
F = 0 Free Brownian particle
m˙
v + v F(x) = ⇥(t)
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Mesoscale regime
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2
3
4
5
6
7
0
Ab initio
Atomistic
Continuum
Number of atoms Simulation
Coarse grained length scales.
Coarse grained time scales.
Retain thermal fluctuations.
Mesoscale methods
}
Examples
Brownian dynamics.
Dissipative particle dynamics.
Time-dependent Ginzburg-Landau.
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Coarse-graining in degrees of freedom
What is the idea ?
x1
x2
} P(x1, x2
)
RV y = x1
+ x2
“Coarse-grained” sum
P(y)
P(y) = dx1dx2
(y x1 x2
)P(x1, x2
)
What is the distribution ?
contains less information about the system than
P(y) P(x1, x2
)
Adequate if we are only interested in the sum variable.
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General ‘coarse-graining’ formula
P(x1, x2, . . . , xN
) y = f(x1, x2, . . . , xN
)
Microstate probability Mesoscale variable/order parameter
P(y) =
⇥ N
i=1
dxi
[y f(x1, . . . , xN
)]P(x1, . . . , xN
)
Mesostate probability
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Coarse-grained Landau-Ginzburg functional
Microscopic Hamiltonian Gibbs distribution
P(q) =
exp[ H(q)]
Z
H(q)
= f(q)
Order parameter Definition of Landau functional
P(⇤) =
⇥ N
i=1
dqi⇥[⇤ f(q)]
exp[ H(q)
Z
⇥
exp[ L]
Z
P(⇥) ⇥
exp[ L]
Z
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Explicit DOF coarse-graining ...
H(s1, s2, . . . , sN
) = J
ij⇥
sisj
Order parameter.
Block spin.
Coarse-grained
magnetization.
=
1
N
i
si
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Explicit DOF coarse-graining ...
H(s1, s2, . . . , sN
) = J
ij⇥
sisj
Order parameter.
Block spin.
Coarse-grained
magnetization.
=
1
N
i
si
P(⇥ ) ⇥
exp[ L]
Z⇥
=?
K. Binder, Z. Phys B, 43, 119 (1981)
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Explicit DOF coarse-graining ...
H(s1, s2, . . . , sN
) = J
ij⇥
sisj
Order parameter.
Block spin.
Coarse-grained
magnetization.
=
1
N
i
si
P(⇥ ) ⇥
exp[ L]
Z⇥
=?
K. Binder, Z. Phys B, 43, 119 (1981)
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Explicit DOF coarse-graining ...
H(s1, s2, . . . , sN
) = J
ij⇥
sisj
Order parameter.
Block spin.
Coarse-grained
magnetization.
=
1
N
i
si
P(⇥ ) ⇥
exp[ L]
Z⇥
=?
K. Binder, Z. Phys B, 43, 119 (1981)
Explicit DOF needs this!
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Or ansatz based on symmetry.
L = A
2
2 + B
4
4 + K
2
(⇥ )2
P(⇥) ⇥ exp[ (A
2 ⇥2 + B
4 ⇥4)]
P(s) ⇥ a+
(s 1) + a (s + 1) -J +J
local part non-local part
K( )2
All equal-time equilibrium properties are determined by this functional.
!! Why is this called a “free energy” ? Is it a thermodynamic free energy ?
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What about dynamics ? Temporal coarse-graining
D = kBT
6⇥ a
Why is this independent of
particle mass ?
⇥d
= m Inertial time scale. Time the
velocity ‘remembers’ its
initial condition.
d
˙
x = v
˙
x = ⇥(t)
Overdamped equations of
motion. Valid when
d
m˙
v + v = ⇤(t)
= 6⌅⇥a
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Overdamped stochastic equations
damping reversible force
fluctuation
deterministic stochastic
mean behaviour ‘root N’ fluctuations
˙
x = ⇥U + ⇥(t)
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Overdamped coarse-grained equations of motion
˙
⇤(r) =
L
⇤
+ ⇥(r, t)
˙
⇥(r) = [A⇥ + B⇥3 K⇥2⇥] + (r, t)
damping reversible force
fluctuation
Model A equation
⇥⇥(r, t)⇥(r , t )⇤ = 2kBT (r r ) (t t )
Fluctuation Dissipation
Relation.
!! Zero-mean
Gaussian noise
(r, t)⇥ = 0
“Stochastic partial differential equations with additive Gaussian noise”
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Conserved order parameters
Ising spin Lattice gas
Ising spins are usually non-conserved
d
dt
(r, t) = 0
Lattice gas models are conserved
d
dt
(r, t) = 0
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Conserved coarse-grained dynamics
damping reversible force
fluctuation
Model B equation
Fluctuation Dissipation
Relation.
!! Zero-mean vector
Gaussian noise
(r, t)⇥ = 0
˙
⇤(r) = ⇤2
L
⇤
+ ⇤ · ⇥(r, t)
˙
⇥(r) = ⇤2[A⇥ + B⇥3 K⇤2⇥] + ⇤ · (r, t)
!! Derive this. Use the local conservation law
˙ + ⇥ · j = 0
⇥⇥i
(r, t)⇥j
(r , t )⇤ = 2kBT ij
(r r ) (t t )
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Numerical solution
Stochastic PDE
Stochastic ODE
Stochastic realisation
Spatial discretisation
Temporal integration
⇤t⇥ = D⇤2
x
⇥ +
⇥x
=
(x + h) (x)
h
⇤t⇥(i) = DL2
ij
⇥(j) + (i)
⇥(i, t + t) ⇥(i, t) =
t+
t
DL2
ij
⇥(j) + (i)
!! Obtain the explicit form of the L matrix for a central difference Laplacian
Conclusion
• Mesoscale methods are appropriate at length scales intermediate between the molecular
and continuum scales.
• The continuum description must be supplemented by fluctuation terms. At the mesoscale,
the number of particles is not so large that fluctuations can be neglected.
• Lengths and times must be coarse-grained. Intelligent coarse-graining improves
computational efficiency, often by orders of magnitude, compared to direct MD.
• Mesoscale methods can be particle-based, for instance dissipative particle dynamics and
Brownian dynamics, or field-based like time-dependent Ginzburg-Landau theory and
fluctuating hydrodynamics.
• TDGL equations can be solved very efficiently on computers using matrix formulations.
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Further reading
• Stochastic processes in Physics and Chemistry : van Kampen
• Handbook of stochastic processes : Gardiner
• Principles of Condensed Matter Physics : Chaikin and Lubensky
• Modern Theory of Critical Phenomena : Ma
• Reviews of Modern Physics article : Halperin and Hohenberg
• Numerical Solutions of Stochastic Differential Equations : Kloeden and Platen.