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Theory, Algorithms and Applications of Dissipative Particle Dynamics
Sept. 21-23, 2015 Shanghai
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Multiscale simulations
Polymer models at coarse-grained (CG) level
Combining different scales in one simulation
Enhanced sampling
Powerful simulation package
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Generic polymer model Dissipative particle dynamics (DPD) :
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Generic polymer model With DPD:
……
……
Block copolymers with different sequences, flexibilities, topologies, and so on.
Polymer grafted nanoparticle with different polymer compositions, nanoparticle shapes, and so on.
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Network morphology
Crossland et al., Nano Lett. 9, 2807, 2009.
Solid-state dye-sensitized solar cell
Advantage: • A large surface/volume ratio of metal oxide • A short diffusion length for exciton to the
interface
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Network morphology
Gyroid structure only forms in a very narrow composition window (~3%).
Hillmyer et al. Prog. in Polym. Sci., 33, 875, 2008. Mahanthappa et al. J. Am. Chem. Soc. 134, 3834, 2012.
Irregular bicontinuous network structure forms in composition window (~10%).
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Network morphology
Whether asymmetric polydispersity is required -- that is whether the lengths of A blocks must be narrowly distributed?
Whether both domains are fully continuous across the entire composition range for which the irregular bicontinuous structure forms?
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Network morphology
uuNNNN
uN
uuNp
nwn
n
uu
)1(PDI ,
)(
)exp()(
1
Schulz-Zimm (SZ) distribution:
Simulated systems:
System PDIA PDIB
Asymmetric PDI 1.0 1.5 (SZ)
Symmetric PDI 1.5 (SZ) 1.5 (SZ)
AxBN-2xAx, Nn= 8~18
Vbox = 40 40 40
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Network morphology
irregular bicontinuous phase (BIC) ~ 10%
PDIA=1.00, PDIB=1.50 (SZ)
Whether the lengths of A blocks must be narrowly distributed?
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Network morphology
Whether the lengths of A blocks must be narrowly distributed?
irregular bicontinuous phase (BIC) ~ 20%
PDIA = 1.50 (SZ), PDIB = 1.50 (SZ)
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Network morphology
Whether both domains are fully continuous across the entire
composition range for which the irregular bicontinuous structure forms?
The BIC structures have good continuity.
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Network morphology
The system of ABA (PDIA=1.00, PDIB=1.50): fB=0.375, cN=62.04
Take a part of the network structure
Show polymer beads
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Network morphology Short middle B block Long middle B block Middle-sized B block
Selective distribution of blocks with different chain lengths can stabilize the BIC phase.
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Soft Janus particle model
Soft Janus particles: Star-like block copolymer with incompatible arms
Soft two-patch (triblock Janus) particles: Small polymer gel with different components and crosslinking densities Percec et al. Science, 328, 1009, 2010.
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Soft colloidal particle model We need to describe patchy particles with a simple model. We have proposed a potential to represent the interactions between two colloidal particles:
as the units.
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Soft colloidal particle model
E: elastic modulus
d: diameter of colloidal particle
Define d: the range of attraction
Substitute rij by d in Uij, we have G: potential well depth
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If we know the modulus of colloid particle (E), the size of the colloid particle (d), the attraction range (d), and the attraction strength (G), we can exclusively define the parameters in our model.
Suppose: nanoparticle diameter d = 20 nm Elastic modulus E = 8.3107 Pa Attraction range d = 0.4 nm Attraction well depth G = 2 kBT
Soft colloidal particle model
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Describe the patch size
for and
The patch parts are hydrophobic.
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Patchy particle self-assembly
G=2.0 kBT; =30o G=9.8 kBT; =30o
We then focus on the soft two-patch particle with diameter d ~ 20 nm and modulus E ~ 4.1106 Pa:
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Patchy particle self-assembly
G=2.0 kBT; =60o G=9.8 kBT; =60o
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Describe patchy particle
The middle part is hydrophobic.
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Patchy particle self-assembly
We then focus on the soft two-patch particle with diameter d ~ 20 nm and elastic modulus E ~ 4.1106 Pa, and build up phase diagram by scanning the attraction well depth G and the surface coverage . The volume fraction is .
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Patchy particle self-assembly
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Patchy particle self-assembly
Loosely packed hexagonal membrane
Tetragonal membrane
Kagome membrane densely packed
hexagonal membrane
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Multi-patch particle model
……
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Multi-patch particle model
We use quaternion method to integrate equations of motion.
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Multi-patch particle model
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Multi-patch particle model
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Multi-patch particle model
(Patch size)
(Att
ract
ion
)
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Combining 2 scales in 1 simulation
Stochastic-reaction-in-a-cutoff method. Can be used to generate polymerization products.
A-B
A and B
Reaction coordinate
Reaction models in CG Simulations
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Stochastic reaction in a cutoff
Advantages: • Simple • Ready to be implemented in generic/CG models
reactive end
free monomers
reaction cutoff
the chosen one …… or not
• Reaction probability Pr : predefined, 0≤Pr ≤ 1.
• Random generator (uniform random number P).
If P Pr, connect;
Else if P > Pr, do not connect.
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Stochastic reaction in a cutoff
……
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Epoxy layer structure on carbon fiber
• Carbon fiber has to be protected by epoxy, otherwise too brittle to use.
• Sizing agent is important to increase the affinity between epoxy layer
and carbon fiber.
• In experiments, it’s difficult to characterize structures and mechanical
properties of this complex.
Epoxy layer sizing agent carbon fiber
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Chemicals in epoxy and sizing agent
DDS:
DGEBA (RA):
Sizing agent (SA):
MC=289.97g/mol
MB=312.40g/mol MA=248.30g/mol
~
3
( ) 266.28g/mol
409.42A
i C iA iM M
v
Length scale: L=1.07nm
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Carbon fiber-epoxy complex
The coarse
grained model
represents a system with more than 10,000,000
atoms
We use DPD to study the influence of reaction on the distribution of different chemicals. The interaction parameters between them are obtained from their c parameters.
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Reaction kinetics
Reaction kinetics:
Typical network structure formed in
curing process
R NH2 + H2C CH R1
O
K1RNH CH2 CH R1
OH×
RNH CH2 CH R1
OH
H2C CH R1
O
+ N
CH2
CH2
CH R1
OH
CH R1
OH
R
K2
×
× CH
OH
+ H2C CH
O
CH
O
H2C CH
OH
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Reaction+diffusion
Composition of different chemicals in these layers
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Time evolution of epoxy groups
Curing process slows
down with time,
because the number of
functional groups
deceases largely with
time and “big”
molecules are difficult
to move.
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Chemical distribution
Chemical distribution along the normal direction of carbon fiber surface.
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Mechanical properties
sample Up
slice Middle
slice Down slice
Shear Modulus
(GPa)
1.217± 0.244
0.804± 0.461
0.527±0.385
Generate all-atom model based on the chemical distribution in different layers;
Run MD simulations and calculate mechanical properties.
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Timescales (Sampling)
It is still difficult to approach equilibrium even with CG representation.
SDK CG model for PEG surfactants.
Klein et al., JCTC, 7, 4135, 2011
0.0 2.0x106
4.0x106
6.0x106
8.0x106
1.0x107
0.30
0.33
0.36
0.39
0.42
0.45
time steps
fA=0.30, cN=26
A7B3 block copolymer model.
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Integrated tempering sampling (ITS)
energ
y d
istr
ibution
Temperature
T1
T2
T3
T4
T5
ITS
energ
y d
istr
ibution
Temperature
T1
T2
T3
T4
T5
ITS
energ
y d
istr
ibution
Temperature
T1
T2
T3
T4
T5
ITS
Generalized distribution:
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Implementation of ITS
For :
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How to obtain nk?
Define the energy Ukp, at which the values of two adjacent terms in W(r) are equal:
Therefore
For energy
The value of W(r) is dominated by its k-th term.
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How to obtain nk?
Uk-1
qU
k
q
Pk+1
(U)
Pk-1
(U)P
k(U)
Po
ten
tia
l e
ne
rgy
dis
trib
uti
on
Potential energy
Pk+1
(U)
Define the energy Ukq, at which the potential energy distribution of the canonical
ensemble at temperature Tk is equal to that of the canonical ensemble at temperature Tk+1 .
Since
So
For energy
there is a maximum for function Pk(U).
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How to obtain nk?
To optimize the energy distribution generated in ITS simulation, when W(r) is dominated by the k-th term in the range of Uk-1
p < U < Ukp, the maximum of
the potential energy distribution should be in the same range:
Thus
The slope of a secant line is approximated by average of the slopes of tangent lines at two line terminals.
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The temperature distribution
Define overlap factor t, which gives the ratio between energy distributions at two adjacent temperatures.
Thus:
Finally we have:
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The temperature distribution
Compare to replica exchange method: In ITS:
If a set of temperatures could give a reasonable acceptance ratio in REM simulations, there should be enough overlap between adjacent temperatures in ITS.
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Simulation procedure
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Coil-to-globule transition
In ITS: t=exp(0.5) T=1.0-4.35 Simulate 1.0X109 steps In conventional MD: 31 temperatures
T
N=100
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GALAMOST: GPU-accelerated large-scale molecular simulation toolkit
GPU simulation package
Functions:
CGMD; Brownian Dynamics; Dissipative
Particle Dynamics;
Particle-field coupling (MDSCF);
Numerical potential (e.g. from iterative
Boltzmann inversion & inverse Monte Carlo);
NVE; NVT; NPT (Nose-Hoover; Andersen);
Anisotropic soft particle model;
Stochastic polymerization model;
Integrated tempering sampling.
http://galamost.com/
Free to download!
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GALAMOST: Structures
Script
UGI
Python
Python Tkinter
C++ CUDA C Users
Call modules Build up modules User interfaces
More characteristics of this package:
Specifically designed for running on GPUs only
Standard format of input and output file: xml, mol2, dcd ...
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GALAMOST: Performances
Performances: the average costing time per time step of GALAMOST and HOOMD. System size: up to 2.2 M LJ liquid particles or 3.0 M DPD liquid particles on GTX 580 with 1.5 GB device memory.
0.0 0.5 1.0 1.5 2.0 2.5 3.0
0.00
0.04
0.08
0.12
0.16
LJ Liquid GALAMOST
LJ Liquid HOOMD
DPD Liquid GALAMOST
DPD Liquid HOOMDti
me
(s)
N/106
DPD: ~1.5 days for 3.0M particles1.0M steps.
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Summary
Approaching larger spatiotemporal scales in polymer simulations:
DPD
Generic polymer model
Stochastic polymerization
model
Soft patchy-particle model
Numerical potential with DPD
thermstating
DPD with
electrostatics
DPD with SCF
treatment
Enhanced sampling
(ITS)
Kinetic network analysis
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Acknowledgement
• Financial supports from National Natural Science Foundation of China.
• Financial supports from Ministry of Science and Technology of China.
• All my group members! • Collaborators:
• Prof. Zhao-Yan Sun and Prof. Lijia An @ Changchun Inst. Appl. Chem. • Prof. De-Yue Yan and Prof. Yongfeng Zhou @ Shanghai Jiaotong U. • Prof. Aatto Laaksonen @ Stockholm U. • Prof. Florian Mueller-Plathe @ TUDarmstadt • Prof. Giuseppe Milano @ Salerno U. • Prof. Yi-Qin Gao @ Peking U. • Prof. An-Chang Shi @ McMaster U. • Prof. Zhihong Nie @ Maryland U. • Prof. Xuhui Huang @ HKUST ……
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Thank you for your attention!
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Changbai mountain in Jilin province