7/18/2014
Multiscale modeling of
Polymer Melts:
Polydimethylsiloxane(PDMS)
Under the guidance of
Prof. Hemant Nanavati
M. Tech Chemical Engineering
Outline

Introduction

Background
Introduction

Polydimethylsiloxane(PDMS)

Motivation for the work

Molecular Dynamics (MD)

Coarse-graining (CG)
Polymer simulation at one scale does not yield

Primitive Path (PP) rheological and thermodynamic properties

Need of multiscale simulation arises

Coarse-grained Molecular Dynamic (CGMD) simulation of PDMS

Atomistic simulation of PDMS octamer

CG potential parameters
PDMS long chain- excellent rheological properties

Coarse-graining of PDMS

Want to add

CGMD via DLPOLY

Equilibration of long PDMS chain
Molecular dynamics (MD) simulation




Determines polymer system’s static & dynamic properties
Production Run
Presented by:
Primitive path analysis using Z1-Code
Pravin Kumar

Z1-Code
Based on the solution of the classical equation of motion 

Calculation of tube radius and tube potential calculates forces on each atoms.

Tube Radius

Coarse-grained (CG) MD potentially superior to atomistic MD
123020036

Tube Potential

Requires less but proper information

Procedure 1

Procedure 2

Conclusion
 7/18/2014

Coarse-graining (CG)
Polydimethylsiloxane (PDMS)
Why CG?

PDMS is a group of monomers  Atomic model contains details of every atom
containing silicon-oxygen skeleton
Simulation  hard to obtain  large number of degree of
with 2 methyl groups attached to freedom
silicon atom. CH3 H3C CH3
CH3

Atomistic simulation  large number of interaction accounted
CH3

Background
How CG?

H3C
Si

Well Studied atomistically at Si Si

Lumping few atoms or molecule  ONE Bead

CH3
H3C
smaller scale. O O

Silicon based organic polymer n

A= [H-(CH3)2-SiO]-

High temperature
viscous liquid B= -[(CH3)2-SiO]-

Low temperature
elastic solid
Structure of PDMS

C= -[(CH3)2-SiO-H]

Application
contact lenses and

Need of Coarse-graining
medical devices to elastomers

Coarse-graining of polymer chain  CG representation of

Using large system of 45,000 reduces number of degrees of freedom PDMS Beads
monomer
system and mol. Wt.
CG simulation  Interaction between the CG beads
effects
 7/18/2014

Primitive Path(PP) Coarse-Grained MD

simulation of PDMS

Objectives:
Representing construction of primitive path
Atomistic Simulation of PDMS octamer
Source: MANSARD, Vincent, Identifying tube in molecular simulation,2009

With reference to the figure

Coarse-Graining Obtain existing CG force-field parameters

Coarse-graining of PDMS 1:1 mapping scheme
a)A polymer (black line) in a network of topological constraints
Obtain Input files for DLPOLY  Run DLPOLY
(dots).
Equilibration (remove memory of initial structure) run
b)The constrains can be replace by a tube (red lines). The axes Gradually introducing CG potentials
of the tube (dashed lines) is called the primitive path.
Primitive path generation using Z1-Code
c)The polymer is constrained in a tube of diameter a, which can
Obtaining tube radius and tube potential distribution
be obtained by radial distances.

PPA
Length of PP, confining tube radius, tube potential,
number of entanglements.
 7/18/2014

Atomistic Simulation of CG potential parameters CG potential parameter Contd..

PDMS octamer
Interaction potential

Bending potential

= 
௕௢௡ௗ௘ௗ + 
௡௢௡ି௕௢௡ௗ௘ௗ
Probability distribution of angle 

Construction of 20 chains of PDMS octamer
௉ ఏ

௕௘௡ௗ = −஻  ln
using polymer consistent force-field (pcff)
Bonded potential  ୱ୧୬ ఏ

Chains were confined in simulation box ‫ܧ‬௕௢௡ௗ௘ௗ = ‫ܧ‬௦௧௥௘௖௛ + ‫ܧ‬௕௘௡ௗ + ‫ܧ‬௧௢௥௦௜௢௡
Bending potential 

Stretching potential  ௞
 ௝௜௞ = (௝௜௞ − ௢ )ଶ+
௞ᇲ
(௝௜௞ − ௢ )ଷ+
௞"
(௝௜௞ − ௢ )ସ

Perform energy minimization ଶ ଷ ସ
‫ܧ‬௦௧௥௘௖௛ = −݇஻ ܶ ln ௉ ௟ ൗ௟మ ܷ‫ݎ‬௜௝ = ݇(‫ݎ‬௜௝ − ‫ݎ‬௢ )ଶ
ଵ

Box subjected to NPT dynamics for ~3ns
volume ଶ
equilibrated

NVT dynamics for ~5ns
pressure equilibrated

Calculation of CG potentials like: length, angle, dihedrals
by Iterative Boltzmann Inversion

Source: Gollapalli V. S., 2011, Multiscale Modelling of polymer melts, M. Tech Thesis, IIT Bombay Source: Gollapalli V. S., 2011, Multiscale Modelling of polymer melts, M. Tech Thesis, IIT Bombay
 7/18/2014

CG potential parameter Contd.. CG potential parameter Contd..

Coarse-graining of PDMS

Coarse graining of PDMS based on bead spring model using

Dihedral Potential

Non-bonded Potential
1:1 mapping scheme

Probability distribution of torsional angle 
Radial distribution function g(r ) of PDMS 
Center of mass coordinates of bead 

௧௢௥௦௜௢௡ = −஻  ln ()
௡௢௡ି௕௢௡ௗ௘ௗ = −஻  ln ( ) ௜ = ∑
௫೔ ∗௠೔
Where:
ெ
 =   

௜ , ௜ , ௜ =   


Dihedral Potential 
Lennard Jones Potential  ௬೔ ∗௠೔
௜ = ∑
U୪୨ r = 4ϵ (஢⁄୰)ଵଶ − ஢⁄୰ ଺ ௜ =   
     ௜ , ௜ , ௜
ெ

௜ , ௜ , ௜ =   
    
ଵ ଵ ଵ
ܷ ∅௜௝௞௡ = ‫ ܣ‬1 + cos( ∅௜௝௞௡ + ‫ ܤ‬1 + cos( 2∅௜௝௞௡ + ‫(ܥ‬1 + cos(3 ∅௜௝௞௡ ) ௭೔ ∗௠೔
ଶ ଶ ଶ
௜ = ∑
ெ

Fig. 4 – CG representation of PDMS octamer

These coordinates CONFIG file for DLPOLY simulation
Source: Gollapalli V. S., 2011, Multiscale Modelling of polymer melts, M. Tech Thesis, IIT Bombay Source: Gollapalli V. S., 2011, Multiscale Modelling of polymer melts, M. Tech Thesis, IIT Bombay
 7/18/2014

FLOW CHART OF CGMD via CGMD via DLPOLY Equilibration Run

DLPOLY OUTPUT

Construction of long chain of PDMS
60chains of
CG potential parameters  Approximation close to actual potential 
Density of the system is not equilibrated to its experimental density.
CONFIG
750monomer via Material Studio

Rescaling of potential needed  According to Kremer

Equilibration run via DLPOLY ௘௫௣௘௥௜௠௘௡௧௔௟ ∗ ௥௘௤௨௜௥௘ௗ
ଷ
= ௦௜௠௨௟௔௧௜௢௡ ∗ ௦௜௠௨௟௔௧௜௢௡
ଷ

Where  is the density and

FIELD REVCON

Initial configuration  New final stable configuration
denotes LJ potential length

CG bonded potentials were introduced 
CONTROL STATIS
Iterative procedure gives us the final targeted density of 0.96g/cc at
DLPOLY
Length potential for 10ps =6.12Å.
REVOLD
Angle potential for another 10ps

Dihedral potential for another 10ps
HISTORY

DLPOLY.Z Non-bonded potentials or LJ potentials were employed

Starting from 1% for 0.1ns  100% of LJ potentials
RDFDAT

INPUT FILES OUTPUT FILES Slowly introducing the potential  time to avoid
overlapping of atoms onto each other
 7/18/2014

Production Run Primitive Path Analysis (PPA) Tube Radius

Density equilibrated structure  NVT dynamics for 12ns
using Z1-Code
Tube generated via reptation will have some radius

Z1-Code  works on the principle of Shortest multiple disconnected
 Pressure of the system is equilibrated.
A  Other chain coordinates
path (SMDP)

X1, X2  Entanglement Point A (a1, b1, c1)

SMDP  Fixing the ends of chain and Contracting them taking care of

ଵ , ଶ  distance between chain coordinates and
ଵ ଶ
uncrossability constraints until they entangled to each other
0.06
entanglement point r
0.04

Chain will appear like shortest multiple disconnected path and
r will be the radius of the tube formed.
entanglement points are obtained.
X2 (x2, y2, z2)
0.02
X1 (x1, y1, z1)
Pressure [GPa]

0
Formula is needed

Entanglement  Chain can reptate like snake  Hypothetical tube
-0.02 generated.
-0.04

r => perpendicular distance from A to X1X2
-0.06
0 2 4 6 8 10 12
Time [Nano Seconds] .
 7/18/2014

Tube Potential Procedure 1 Procedure 1 ..contd

Probability that chain terminates at ‘r’ is ! 
Chain coordinates and entanglement points obtained by Z1-Code

Actual data plots of potential
Introduce to a new procedure as

Probability density Ω(r ) is the ratio of probability to its volume.

Elemental Volume of tube (like a cylinder) is 2#  $

Neglecting the 6 bead near the entanglement point both side
to minimize -6.2 -6.8

!
the 1/r effect. We have

Ω ∝
E -7 E
Tube

-6.4 Tube

Tube Potential [k BT]

Tube Potential [k T]
4
4x10 -7.2

B
-6.6
4

Tube potential is defined as 3.5x10 -7.4

௧௨௕௘ = −%஻ &(Ω )

4
-6.8
3x10 -7.6

Probability P(r)
2.5x104 -7
-7.8
4
2x10 -7.2

These tube potential obtained
fitted to the model equation
-8

 =∗ +
4
1.5x10
ଶ
-7.4 -8.2
4
1x10 0 5 10 15 20 25 30 35 40 0 5 10 15 20 25 30 35 40
Radial Distance from PP [Angstrom] Radial Distance from PP [Angstrom]
5000

0
0 5 10 15 20 25 30 35 40
Radial Distance from PP [Angstrom] By frequency Data By Potential Data
Probability distribution of radial distances from PP of PDMS
 7/18/2014

Procedure 1 ..contd Procedure 2 Procedure 2 ..contd

This procedure involve  considering all bead in the chain and finding
Actual data for potential from frequency

Tube potential distribution the tube radius and tube potential.
6
8x10
6
7x10 -12.5
2 2
E
Tube E 6x10
6 E
Tube Tube

Probability P(r)
E -Model E -Model
Tube Tube
1.5 6
1.5 5x10 -13
Tube Potential [k T]

Tube Potential [k T]

Tube Potential [k T]
B

B
6
4x10
1 1
o 6 -13.5
Tube Radius = 26.0316 A 3x10
Tube Radius = 26.0575Ao
0.5 0.5 2x106
-14
6
1x10
0
0 5 10 15 20 25 30 35 40
0
0 5 10 15 20 25 30 35 40 0 5 10 15 20 25 30 35 40 Radial Distance from PP [Angstrom] -14.5
Radial Distance from PP [Angstrom] Radial Distance from PP [Angstrom]

Probability distribution of radial distances from PP of PDMS 0 2 4 6 8 10 12

Radial Distance from PP [Angstrom]
By frequency Data By Potential Data
 7/18/2014

Procedure 2 ..contd Summary and Future work

Tube potential distribution by frequency data
We have carried out
 Coarse-grain molecular dynamics using existing thesis force field
parameter for a large system
4

3.5 E  Primitive path analysis of the equilibrated structure using new

Tube
E -Model algorithm Z1-CodeFinding out the tube radius
3 Tube
Tube Potential [k T]

We find out tube radius following various procedures.

B

2.5

2

We need to carry out in the future
1.5

1
 Analyzing the shape of polymer with the help of radius of gyration
('௚ )
0.5 Tube Raidus = 6.551 A
o

0
0 2 4 6 8 10 12
Radial Distance from PP [Angstrom]
 7/18/2014

Objectives

Coarse-Graining of
Atomistic Simulation Obtain the existing
PDMS as 1:1
of PDMS octamer force field parameter
mapping

Generating amorphous
cell of 60 chains and
750 monomer