Analyzing Graphene Vibrations via Molecular Dynamics

Simulations and Dimension Reduction Techniques

Hind Almisbahi

Supervisor: Dr. Lilian Tang

Co-supervisor: Dr. David Faux

Transfer Report

Department of Computing

Faculty of Engineering and Physical Sciences

University of Surrey

January, 2014
Abstract

This research studies the atomic vibrations of graphene using the molecular
dynamics simulation and dimension reduction techniques. Lammps is used to
conduct simulation of graphene sheet composed of 2508 carbon atoms at room
temperature. AIREBO potential function is used to model the atomic interactions.
Correlation functions of the produced trajectories are used to extract the atomic
vibrations. Low frequency vibrations are extracted from displacement correlation
function while high frequency vibrations are extracted from velocity correlation
function. The dimension reduction technique PCA is used to visualize the nature of
the low frequency vibrations.

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Table of Contents

Abstract...................................................................................................................... i
Table of Contents .......................................................................................................ii
List of Figures ............................................................................................................ iv
List of Tables ............................................................................................................. iv
Abbreviations .............................................................................................................v
Physical measurement units .......................................................................................v
1 Introduction ........................................................................................................... 1
1.1 Importance of Graphene .................................................................................. 1
1.2 Molecular dynamics ......................................................................................... 2
1.3 Dimension reduction ........................................................................................ 3
1.4 The study approach and research aims ............................................................ 4
2 Graphene ............................................................................................................... 5
2.1 Structure of graphene ...................................................................................... 5
2.2 Properties and applications of graphene .......................................................... 7
2.3 Lattice defects .................................................................................................. 8
3 Simulation and analysis tools ................................................................................ 10
3.1 Molecular dynamics ....................................................................................... 10
3.1.1 Potential function ................................................................................... 11
3.1.2 Periodic Boundary Conditions ................................................................. 12
3.1.3 Ensembles ............................................................................................... 13
3.1.4 Time step ................................................................................................ 14
3.2 Lammps ......................................................................................................... 14
3.3 Correlation functions ..................................................................................... 15
4 Analysis of atomic motions via dimension reduction ............................................ 18
4.1 Principal Component Analysis (PCA) ............................................................... 18
4.2 Filtering the motions ...................................................................................... 19
4.3 Limitation of PCA ........................................................................................... 20
5 Results and discussions......................................................................................... 21
5.1 Equilibration .................................................................................................. 21
5.2 Correlation functions and phonon density of states results ............................ 22

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 5.3 PCA and nature of motions ............................................................................ 25
6 Conclusion and future work .................................................................................. 30
6.1 Contributions ................................................................................................. 30
6.2 Future work ................................................................................................... 31
Bibliography ............................................................................................................ 32

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List of Figures

Figure 1: Different types of scattered light from a material [12]. ............................... 3

Figure 2: Atomic structure of graphene [18]. ............................................................. 6
Figure 3: Valence orbitals of carbon in graphene [20]. ............................................... 7
Figure 4: Graphene sheet with one vacancy defect [29]. ........................................... 9
Figure 5: Bonded interactions between atoms [35]. ................................................ 11
Figure 6: Periodic Boundary Conditions in three dimensions [42]. ........................... 13
Figure 7: (a) graphene phonon dispersion relation. (b) graphene phonon DOS [56]. 17
Figure 8: Time dependent fluctuation of (a) temperature, (b) potential energy, (c)
pressure. ................................................................................................................. 21
Figure 9: Diplacement correlation function. ............................................................ 23
Figure 10: Fourier transform of displacement correlation function. ......................... 23
Figure 11: Velocity correlation function. .................................................................. 24
Figure 12: Fourier transform of velocity correlation function................................... 24
Figure 13: Fourier transform of force correlation function....................................... 25
Figure 14: Scree plot of eigenvalues against eigenvectors. ...................................... 26
Figure 15: Diplacement correlation function of R1. .................................................. 26
Figure 16: Fourier transform of displacement correlation function of R1. ................ 27
Figure 17: Diplacement correlation function of R2. .................................................. 28
Figure 18: Fourier transform of displacement correlation function of R2. ................ 28
Figure 19: Highliting the positions of peak 564 cm-1 (Band A) and peak 1624 cm -1
(Band B) in comparision to the equivalent vibrations of reference [56]. .................. 29

List of Tables

Table 1: Structure of the position trajectory matrix X. ............................................. 18

Table 2: Mean and standards deviation values of temperature, potential energy, and
pressure at the last 9000 fs. .................................................................................... 22
Table 3: Time plan of the future work...................................................................... 31

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Abbreviations

AIREBO= Adaptive Intermolecular Reactive Empirical Bond-Order

DOS = Density Of States
Lammps= Large-scale Atomic/Molecular Massively Parallel Simulator
MD = Molecular Dynamics
PBC= Periodic Boundary Conditions
PCA= Principal Component Analysis
REBO= Reactive Empirical Bond-Order
VAF= Velocity Autocorrelation Function
VMD= Visual Molecular Dynamics

Physical measurement units

cm= centimeter
fs= femtosecond
K= Kelvin
Kbars = kilo bars
m= meter
mg= milligram
N= newton
nm= nanometer
Pa=Pascal
ps= picosecond
s=second
TPa=TeraPascal
V= Volt
W= Watt

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1 Introduction

Molecular dynamics (MD) simulation is an important tool to investigate the

characteristics of physical materials and to provide information about the
interactions of atoms and molecules in materials. It has been successfully applied to
predict materials' properties that have high correlation to the experimental
measurements. It can be used to visualize the change of materials' shape under
various conditions.

Graphene is a two dimensional material composed of one layer of carbon atoms. Its
physical and chemical properties have attracted a lot of research interests which
make it a candidate for a large number of applications.

Molecular dynamics (MD) simulation is excellent to study the properties and

vibrational modes of the graphene under controlled conditions to understand how
these properties would change with different lattice defects. As the materials get
more complex and have larger number of atoms, the MD produces huge amounts of
data that need better analysis tools. Long period of simulation of a complex matter
produces high dimensional trajectory data that are difficult to interpret only based
on the human intuition. Therefore, machine learning techniques for dimension
reduction potentially provide excellent tools to simplify the interpretation of such
data.

1.1 Importance of Graphene

Graphene is a fascinating honeycomb lattice made of carbon atoms. This material is

one-atom thick layer of the graphite [1]. It shows amazing chemical and physical
properties. It is stronger than steel, stretchable, light, and transparent [2, 3].
Graphene also is a conductor of electricity and heat [1, 4].

Research on transport measurements of graphene reported its extremely high

electron mobility that exceeds 1.5 * 104 cm2/V.s at room temperature [5]. This
property makes the graphene excellent material for the electronic and optical
applications such that it can replace the silicon [1, 5].

The thermal conductivity of graphene at room temperature is reported to be in the

range (4.84 ± 0.44) × 103 to (5.30 ± 0.48) × 103 W/m.K [6]. This high thermal
conductivity makes graphene attractive for the thermal management of
optoelectronics and photonics.

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Graphene has unique mechanical properties. It has Young’s modulus of 1 TPa [3].
The breaking strength of graphene is measured to be 100 times higher than steel
film of the same thickness [7]. It is very light material; its density is approximately
0.77 mg/m2. The mechanical properties of graphene make it excellent material for
the development of lighter cars, planes, satellites, and aircraft [7].

Graphene as a crystalline material has a crystal structure that is repeated

periodically. The atoms are arranged in fixed distances. If the arrangement of these
atoms is not perfect, we have defect. Vacancy defect is the defect that caused by
missing an atom at single point of the lattice [8]. The properties of the graphene can
be controlled or modified based on the defects. For example, the electrical
conductivity of the graphene can be increased based on the vacancy defects [9].

1.2 Molecular dynamics

Molecular dynamics is a computer simulation that studies the motion of system of

atoms and calculates the positions, velocities, and direction of atoms throughout the
simulation time [10]. It depends on solving Newton's equations of motion of the
atoms. The simulation produces the trajectories of atoms and macroscopic
properties of the system such as temperature, pressure, kinetic energy, and
potential energy.

Valuable information about the simulated system resides in the trajectories and
velocities of the atoms throughout all the simulation steps. However, the
interpretation of these data is not straightforward and cannot depend only on the
researcher's intuition. Further analysis should be performed to extract useful and
understandable results of the simulation.

The Velocity Autocorrelation Function (VAF) is calculated from the velocities of

atoms during the simulation steps. It is used to investigate the vibrational properties
of the system. Taking the Fourier transform of VAF produces the vibrational
spectrum of the system. Extracting the vibrational spectrum of the simulated system
under controlled conditions provides researchers the opportunity to study the effect
of various factors such as lattice defects on the simulated system. On the other
hand, it is possible to extract some of the vibrational spectra experimentally using
Raman spectroscopy which is an analytical technique that can be used to study the
vibrational modes of a system. It depends on the interaction of laser light and the
sample under investigation and detecting the scattered light [11]. Figure 1 shows
how materials interact with light. If the energy of the scattered light equals to the
energy of incident light, it is called Rayleigh or elastic scattering. When the scattered

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light has lower energy than the incident light, it is called Stokes Raman scattering. On
the contrary, when the scattered light has higher energy than the incident light, it is
called anti-Stokes Raman scattering. Only small amount of the scattered light differs
in its energy from the incident light due to the interaction with the molecular
vibrations of the system. Hence, some of the vibrational spectrum extracted from
the simulation can be compared to experimental Raman spectra to make further
investigation on the system.

Figure 1: Different types of scattered light from a material [12].

1.3 Dimension reduction

In a system composed of hundreds or thousands of atoms, we have large amounts of

variables that describe the geometry and motion of the molecular systems which
complicate the interpretation of these data. The need to reduce the dimensionality
of the data without affecting the extraction of important results is crucial. The
process of transforming high dimensional data to a space with lower number of
dimensions can be linear dimension reduction or nonlinear dimension reduction.
Principal Component Analysis (PCA) is an example of the linear approach. It is a
powerful technique to reduce the dimensionality of the data and retain its quality in
the same time. Moreover, PCA is an effective technique to identify the global
collective motions of atoms. It produces uncorrelated variables called principal
components from matrix of correlated variables [13]. The components are ordered
in descending manner based on their variances. The first principal component
corresponds to the motion with the highest magnitude [14]. Recovering the
trajectory data based on the first component simplifies the analysis of the atoms'

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motion along that component. There are only few principal components with high
variances, which means that they convey most of the important information.

1.4 The study approach and research aims

The main purpose of this study is to investigate the effect of vacancy defects in
graphene on its vibrational spectrum and atoms' motion using molecular dynamics
simulations and dimension reduction techniques.

Simulation of perfect graphene sheet is conducted using Lammps [15]. The graphene
sheet is composed of 2508 carbon atoms. The simulation is at room temperature, i.e.
300 K and carried out using NVT ensemble. The duration of the simulation is 10 ps
such that every time step is 0.1 fs. The main analysis done on the simulation results
includes calculating correlation functions, taking their Fourier transform to analyze
their vibrational spectra, and extracting principal components to analyze the nature
of atoms' motions.

The specific aims that will be achieved subsequently are as following:

 The effect of different patterns of vacancy defects on graphene will be

simulated. These patterns are even and odd vacancies.
 The vibrational spectra of these different patterns will be calculated and
compared with the spectra of the perfect graphene sheet. Also, our results
will be compared with the published researches that study the vibrations of
graphene.
 Linear motions of atoms will be filtered from the atoms' positions using PCA
and then visualized on VMD to analyze their nature.
 A nonlinear dimension reduction technique such as Isomap will be sued to
analyze the nonlinear motions of atoms.

This report is divided into six chapters. Chapter 1 introduces the research field and
purpose. Chapter 2 provides brief background of graphene structure, properties, and
applications. It also reviews the effect of lattice defects on graphene properties.
Background of MD and Lammps are presented in chapter 3 in addition to the
analysis tools applied to the simulation results such as correlation functions and
Fourier transform. Chapter 4 provides an overview of PCA and its effective role for
analyzing linear atoms motions. In chapter 5, we present and discuss the results of
the simulation of perfect graphene sheet. Chapter 6 concludes the research and
presents the future work.

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2 Graphene

Graphene attracted high attention in the recent years due to its exceptional
properties and the wide range of its applications. It is a two dimensional honeycomb
lattice composed of carbon atoms. The word graphene was introduced in 1986 by
Boehm et al [16] and it was first isolated in the lab in 2003. This work was first
published in 2004 [17]. Andre Geim and Konstantin Novoselov are the two
researchers who isolated this material, at The University of Manchester, and they
won the Noble Prize in physics for this work in 2010 [7]. Since its first isolation,
research exploded on graphene to study its properties and potential applications.

2.1 Structure of graphene

Graphene is formed of carbon atoms arranged in regular hexagonal lattice. The

length of carbon-carbon bond is about 1.42 Angstrom [7]. Figure 2 represents the
structure of 0.9 x 0.9 nm sheet of graphene that is composed of 24 carbon atoms
and 7 hexagons [18].

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 Figure 2: Atomic structure of graphene [18].

As shown in Figure 2, each carbon atom is connected to three other carbon atoms
via sp2 bonds. In fact, carbon atom has six electrons. These electrons occupy two
principal shells. The first shell is fully occupied with two electrons in 1s orbital and
these two electrons are called core electrons. The core electrons are not involved in
bonding. The second principal shell is occupied by the other four electrons and they
are called the valence electrons. The orbitals of the second shell are 2s, 2px, 2py, and
2pz. In graphene systems, one 2s orbital and two 2p orbitals (2px and 2py) are mixed
to form three in-plane sp2 hybridized orbitals. The three sp2 hybridized orbitals
(occupied by three valence electrons) form three sigma covalent bonds δ that are
responsible for the strong bonding between carbon atoms leading to the strength
and the exceptional mechanical properties of graphene. Hence, each carbon atom is
connected to three in-plane neighbours which forms the hexagonal structure of
graphene. The angle between the bonds is 120˚ [19]. The fourth electron of the
second principal shell occupies 2pz orbital which is perpendicular to the graphene
plane and makes π covalent bond which determines the electronic properties of
graphene [20]. Figure 3 shows the carbon valence orbitals.

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 Figure 3: Valence orbitals of carbon in graphene [20].

2.2 Properties and applications of graphene

The unique structure of graphene and its exceptional properties excite the
researchers to study this promising material and explore its potential applications in
various fields.

Electronic transport properties of graphene attract the attention of researchers due

to the wide range of applications that may utilize these properties of graphene. The
electronic band structure of a solid material describes the energy bands that are
allowed to be occupied by valence electrons and the forbidden bands or band gaps
that are not allowed to be occupied by valence electrons. The energy bans (allowed
to be occupied by electrons) are classified into valence bands and conduction bands.
The valence band is the range of energies where valence electrons reside when the
temperature is 0 K. The conduction band is the range of energies where the
delocalized electrons can move freely. The band gap is the range of energies where
no electron can exist and it represents the difference between the valence and
conduction bands. The conduction bands are above the valence bands separated by
the band gap. When the temperature is more than 0 K, some of the electrons may
promote from the valence band to the conduction band based on the material
properties. When the electrons promote, they leave holes in the valence band.
These free electrons and holes are called mobile charge carriers, and their
concentration and velocity have strong effect on the conductivity of the material.
The band gap determines the energy required to free an electron from the valence
band to the conduction band [21, 22, 23]. The materials can be categorized in their
conductivity based on their band gap. Graphene is called a zero band gap
semiconductor because its conduction band and valence band are connected. The
charge carriers' mobility of graphene is reported to be 20,000 cm2/V.s at low
temperatures [24]. Graphene with its high mobility and current density outperforms
the other semiconductors such as silicon [5]. In addition to its high electrical

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conductivity, graphene has high thermal conductivity which makes it potential
material for the thermal management applications [6].

Graphene has amazing mechanical properties. Experiments conducted by a research

group at Columbia University reported that graphene is the strongest material ever
measured. The breaking strength of the defect free sheet of graphene is 42 N/m [3].
The high Young’s modulus of graphene, 1 TPa, make it the stiffest known material. It
is also very stretchable and light [7].

All these promising properties of graphene increase the interest to use it in different
applications. One of the areas where graphene can be used is optical and electrical
applications such as touch screens, liquid crystal displays, and solar cells [7]. The
fabulous mechanical properties of graphene prompt the researchers to use it to
create composite materials that can replace steel in the manufacturing of cars,
satellites, and aircraft [7]. Graphene can also be used in biological applications such
as DNA sequencing [25], mammalian, and microbial detection [26]. It can be used
also for gas sensors [7] and water filtration systems [27].

2.3 Lattice defects

The violation of the regular arrangement in the unit cells of lattice converts it from
ideal lattice to defected lattice which modifies some of the lattice properties. There
are many types of lattice defects based on the dimensionality of the defect. The zero
dimensional defects are called point defects, while the one and two dimensional
defects are called linear and surface defects respectively. Vacancy defect is a kind of
the point defects which has missed atom. The defect in some point of a lattice
causes the lattice's atoms near the defect to displace from their equilibrium
positions in the ideal lattice [8]. Vacancy defect, in addition to adatoms defect (an
atom placed on lattice), is one of the most probable defects that exist in graphene
[28]. Figure 4 shows a graphene sheet that has one vacancy.

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 Figure 4: Graphene sheet with one vacancy defect [29].

The exceptional electronic and mechanical properties of a perfect graphene sheet

decreased or modified in the defected sheets. However, this effect is desirable for
some applications such that the properties are tailored as needed.

The effect of lattice defects on graphene properties has been studied by many
researchers. Banhart et al [30] reviews the effect of defects on the chemical,
electronic, magnetic, and mechanical properties of graphene. It is found that the
vibrational modes of graphene are affected by the vacancy defects [31, 32]. Jack et al
found that the presence of vacancies in specific patterns throughout graphene sheet
can be used to control the direction and dynamical behavior of its fracture [33]. This
is useful to create graphene nanostructures with specific and precise dimensions at
the nano scale. However, a molecular dynamic simulation performed using AIREBO
potential in Lammps found that the vacancies can cause strength loss in graphene
and this loss is dependent on the temperature [29].

Graphene cannot replace silicon in electronics due to its zero band gap.
Nevertheless, lattice defects can be used to open the band gap and make it tunable.
Jafri et al [9] found that vacancies enhance the conductivity of graphene. However,
this effect is working below some threshold such that the addition of more defects
after that threshold will reduce the conductivity. They found that the vacancies
reduce the resistivity of graphene at 0 K temperature. The same threshold exists
here such that the resistivity will grow if the defect concentrations are above specific
threshold.

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3 Simulation and analysis tools

3.1 Molecular dynamics

Molecular dynamics is the study of molecular systems' motions and properties using
Newton's equations of motion. It results in a trajectory which consists of positions
and velocities of particles in successive time steps. The trajectory is calculated by
integrating the Newton's second law of motion:

(1)

Where , mi, and Fi are the position vector, mass, and Force on the particle i. The
integration is broken into steps separated by small and fixed period of time dt. At
every step, the force act on each atom is calculated as a vector of its interaction with
the other particles. The integration over successive intervals of time is called finite
difference method. There are many algorithms that depend on this method such as
Verlet algorithm and leap-forg algorithm [34]. All the finite difference method's
algorithms approximate the positions as Taylor series expansions.

The force field function is the heart of a molecular dynamics simulator. It is

calculated based on the potential energy function which describes the atomic
interactions as a function of the atoms positions.

(2)

Where are the positions ( ) of N particles such that and

is the potential energy function. As the formula of the potential energy
indicates, it is a function of the particles' positions. Generally, the interactions that
contribute in the potential function are non-bonded interactions and bonded
interactions. The non-bonded interaction consists of electrostatic and Van der waal
interactions. The bonded interactions consider the bonds between atoms including
bond stretching, angle bending, and torsion around a dihedral angle (bond rotation)
[34]. Figure 5 shows the bonded interactions between atoms.

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 Figure 5: Bonded interactions between atoms [35].

3.1.1 Potential function

The specific functionality of the atomic interactions depends on the identity and the
physical properties of the simulated system. One of the simplest potentials is
Lennard-Jones potential which is a long-range, non-bonded interatomic potential
[36]. It was first proposed in 1924 and is used to model systems of non-bonded
atoms. Lennard-Jones potential is not accurate to model the covalently modeled
carbon atoms, hence, does not model the accurate behavior of graphene. Reactive
Empirical Bond-Order (REBO) potential was one of the potentials that are developed
to model carbon systems. It has the ability to describe the single, double, and triple
bond energies in carbon systems. It allows covalent bond breaking and formation
which makes it ideal for some types of lattice defects. Due to some drawbacks in
REBO potential, an extension of this potential was developed by Stuart et al [37] and
it is called Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO). AIREBO
extends REBO by adding the non-bonded interactions which are not addressed in
REBO and adding torsional interactions which are important to model curved
structures such as carbon nanotubes. Hence, AIREBO is the summation of the
following three potential energies: EREBO to model the bonded interactions, ELennard-
Jones
to model the non-bonded interactions, and ETorsional to model the torsional
interactions.

(3)

To model the bonded interactions between atoms i and j, considers a cut-off

function f(rij) such that atoms i and j interact only when the distance between them
rij is less than a specific cut-off value. This will limit the interactions to the nearest
neighbour. The C-C cut-off recommended by Stuart et al [37] is 2 Angstroms and this
is the value we used in our simulation. composed of repulsive and
attractive potentials:

(4)

Where, bij is to model the bond order term and it takes into account lattice defects
[38].

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 is the non-bonded potentials which is calculated also based on a cut-off value:

(5)

Where, is the Lennard-Jones 12-6 potential between atoms i and j, and f(rij) is the
cut-off function that limit the distance at which the interactions are calculated. This
cut-off is important to consider in the simulations of multi-layer graphene systems.
In our simulation, we have one layer graphene sheet. However, we determine cut-
off that can handle the non-bonded C-C interactions in case of defects. Lammps
allows the user to decide the value of a variable called scale factor. This scale factor
is used by Lammps to calculate the cut-off by multiplying the scale factor by sigma
constant included in the AIREBO text file. AIREBO text file includes parameters that
are optimized by the authors of the potential. The sigma constant of C-C interactions
is 3.4. We have chosen the scale factor to be 3. Hence, in our simulation the cut-off is
10.2 Angstroms [15].

The last term of AIREBO is that calculates the four body tensional
interactions which consider the dihedral angles.

Wang et al [29] used AIREBO to study effect of defects on the graphene's strength of
fracture. He studied two types of defects: vacancy defect and Stone–Wales defect,
AIREBO is used only to study the vacancy defect. Lehtinen et al [39] used REBO which
is part of AIREBO to study the vacancy defects of graphene. Also [40, 41] used REBO
to study oscillations of graphene.

This research used AIREBO potential to study vacancy defects on graphene system.

3.1.2 Periodic Boundary Conditions

The simulation of small number of particles suffers from the boundary effects caused
by finite system size. Periodic Boundary Conditions (PBC) are used to simulate the
finite system as an infinite one. This approach means that the molecular system with
finite number of particles is considered as a unit cell that is surrounded periodically
by an infinite number of replicas in the three dimensions. All the replicated unit cells
have the same content. The atoms that leave one side of the unit cell are
compensated by identical copies that enter from the opposite side. The idea of PBC
is shown in Figure 6. Only the behavior of one unit cell has to be simulated and all
the other replicas have the same behavior.

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 Figure 6: Periodic Boundary Conditions in three dimensions [42].

3.1.3 Ensembles

In the molecular dynamics simulation there is a need to control some of the

properties. Depending on which property needs to be constant, different statistical
ensembles are defined. The ensemble is a group of particles that have the same
macroscopic states and different microscopic states (such as positions and velocities
of particles). The macroscopic properties are calculated by averaging over the
particles of the ensemble. Microcanonical ensemble NVE is the simplest and most
fundamental statistical ensemble. It represents an isolated system with constant
number of particles N, volume V, and energy E. The disadvantage of NVE ensemble is
that the real life experiments are not performed under the condition of constant
energy [43]. Other control variables can be used to reflect the real life experiments
such as the temperature. NVT is canonical ensemble which has constant number of
particles N, volume V, and temperature T. It controls the temperature during the
simulation. Lammps implementation of NVT applies time integration on Nose-
Hoover equations of motions and it updates atoms' velocities and positions every
timestep [15]. Numerical experiments done by Evans D. et al [44] demonstrate that
the error of the autocorrelation functions calculated based on Nose-Hoover
thermostat is inversely proportional to the system size i.e. number of particles of the
simulated system [45]. NVT is the ensemble used in our simulation.

The stability and equilibration of the simulation can be monitored by looking at the
variations of the energy and pressure values throughout the simulation steps [10].
Another metrics that can be used to monitor the stability of our simulation are the
observables that we are investigating such as the vibrational spectra.

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3.1.4 Time step

Time step is the time between two successive simulation steps. It should be selected
based on the highest frequency mode in the simulated system. This corresponds to
the shortest vibration period [46]. Time step should be less than 10% of the atomic
vibration period [47]. The time steps used with carbon nanotubes range from 0.15 fs
to 15 fs [47]. Zhao et al [48] used time step of 0.1 fs to study "temperature and
strain-rate dependent fracture strength of graphene". Higher time steps increase the
computational efficiency but reduce the stability of the system, while small time
steps increase the accuracy of the simulation. The time step used in our simulation is
0.1 fs.

3.2 Lammps

Many classical force fields are developed to investigate the properties of the
molecular systems. Lammps is free and open source software that is widely used for
classical molecular dynamics simulations [15]. It has potentials of soft materials and
solid states materials. It is originally developed by Steve Plimpton and currently
maintained by developers and researchers at Sandia National Laboratories. The
word Lammps stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

Lammps input script consists of four parts:

 Initialization: this part includes the definition of units, boundary conditions,

and simulation dimensions. The metal units should be used with AIREBO
potential. In the metal units system Angstrom is used for distance,
picoseconds for time, and electron-volts for energy.
 Atom definition: this part defines the structure of atoms which can be
created by Lammps commands or can be read from a data file which
determines the geometry and types of atoms.
 Settings: this part defines the potential type, output options, and simulation
parameters. The output options set the output file type, variables to be
printed, and how many steps between every two successive prints. The
simulation parameters include neighbour lists, timestep, minimization style,
temperature, and ensemble.
 Run a simulation: this part issues the command to perform the molecular
dynamics simulation.

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Regarding to the output, Lammps prints the thermodynamic information (step,
temperature, pressure, kinetic energy, potential energy, and total energy) of every
step in a log file. It prints also dump files of atoms coordinates, velocity, forces, and
other per atom quantities. The format of these dump files have XYZ, CFG, or other
formats.

Visual Molecular Dynamics (VMD) software has been used in the simulation of this
research to construct the atoms geometry of the input file and to visualize the
simulation output. VMD is molecular modeling and visualization software that is
developed by a group at the University of Illinois and the Beckman Institute [49].
VMD supports more than 60 molecular file formats [50] including Lammps files.

The following setting was used in the simulation of this research:

 A graphene sheet of 2508 was built by VMD.

 The timestep equals to 0.1 fs, the metal units, and AIREBO potential were
chosen.
 Periodic boundary conditions were applied in the x and y dimensions while
the z dimension is fixed.
 Initial structure of graphene sheet was energy-minimized by the method of
steepest descent.
 NVT ensemble was used to equilibrate the sheet at 300 K temperature for 10
ps.
 The thermodynamics information were printed in log file every 10 steps.
 The geometries and per atom quantities were dumped in XYZ and CFG files
every 10 steps.

3.3 Correlation functions

Molecular dynamics simulations produce information about the system every time
step such as positions and velocities of the simulated system. These data can be used
to calculate time dependent properties via time correlation functions.
Autocorrelation functions are special class of correlation functions that measure how
much the variable at time t + t0 is correlated with its value at time t0. On other
words, the autocorrelation functions measure to which degree the system
memorizes its previous values [10, 34]. The spectra measured experimentally by
spectroscopic techniques are the power spectra of dynamical variables which can be
calculated by the correlation functions. This connection between theory and
experiments makes the molecular dynamics simulations valuable tool to study the
structure and dynamical behavior of molecular systems [51].

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Velocity Autocorrelation Function (VAF) is one of the time correlation functions that
measures the correlation between the velocity of an atom at time t + t 0 and time t0. It
can be used to calculate the vibrational spectra of the systems. VAF can be
calculated as following:

(6)

Where T is the simulation's duration and is called the lag time. However, in the
molecular dynamics simulations v(t) is not a continuous function, and its values are
discrete values obtained from a simulation of a number of steps [52]. Given a
simulation of M steps, VAF can be calculated using the following equation:

(7)

The denominator is used to normalize the function [52]. The value v(tn) is calculated
by the subtraction of the velocity temporal average <v n> from the velocity of atom n
at all the time steps i.e. each atom has one <vn> that is the average of that atom's
velocity at all the time steps. The calculated <v n> is subtracted from the velocity of
atom n at every time step. This equation can be used with any dynamical variable
such as atoms' positions [53].

Fourier transforming velocity correlation function provides the phonon density of

states (DOS), or vibrational density of states. Fourier transform of an integrable
function f(x) is:

(8)

Where, x represents time and k represents frequency. Expressing the Fourier

transform in terms of cosine and sine transforms is as following [54]:

(9)

For a discrete function f(n), Fourier transform can be calculated based on the
following equation:

(10)

Where, k = 0, 1, 2, …. , N-1 [55].

Applying equation (10) on VAF(m) produces phonon DOS which shows the allowed
vibrational modes that describe the atomic motion of the system. These vibrational
modes are grouped into various phonon branches that are defined by the number of
atoms in the unit cell. These branches are classified into acoustic branches (related
to waves at long wavelengths) and optical branches (related to waves at short
wavelengths). In addition, they are classified into longitudinal and transverse

16
branches based on their propagation direction such that in the longitudinal branches
the atoms displacement is in the same direction of the wave while in the transverse
branches the atoms displacement is perpendicular to the direction of the wave [19].
The plot that shows these branches is called phonon dispersion relation. In
graphene, all the longitudinal waves are in-plane while some of the transverse waves
are in-plane and others are out-of-plane. These waves are represented by symbols
such that T corresponds to transverse, L corresponds to longitudinal, A corresponds
to acoustic, O corresponds to optical, and Z corresponds to out-of-plane transverse
wave. Hence, e.g. TA means transverse acoustic branch of vibrational modes and ZO
means out-of-plane transverse optical branch of vibrational modes. Figure 7 shows a
typical phonon DOS and phonon dispersion relation of graphene.

Figure 7: (a) graphene phonon dispersion relation. (b) graphene phonon DOS [56].

These phonon branches have relation to the atomic interactions of the system.
Longitudinal branches represent bond stretching interactions [19] while transverse
branches represent bond bending interactions [56].

17
 4 Analysis of atomic motions via dimension reduction

Atomic motions are important to identify and study characteristics of materials.

Atoms' vibrations have specific relation to the bonds that connect atoms and the
atomic structure of the material [57]. The atomic vibrations are represented by
waves of different frequencies and amplitude that flow along the atoms and they
affect atoms displacements.

Molecular dynamics simulations allow investigation of atomic motions by analyzing

trajectories of atomic positions. The accuracy of this analysis is affected by the
potential function used to calculate the force fields. One of the approaches to
analyze atomic motions is using Principal Component Analysis (PCA). Diagonalization
of the covariances of the trajectories results in eigenvalues and eigenvectors that
represent the important atomic motions [14].

4.1 Principal Component Analysis (PCA)

PCA is a dimensionality reduction technique that calculates uncorrelated variables

called principal components from correlated variables [13]. PCA can be calculated
based on the covariance matrix of the trajectory data.

Assuming that we have N particles and a simulation of M steps, X is an (M * 3N)

trajectory matrix that presents the atoms positions in three dimensions: x, y, and z.
Each row of X has the positions of all the atoms during one step, and each column of
X has the evolution of the atom position throughout the simulation steps at one of
the dimensions. Table 1 presents the structure of X.

Table 1: Structure of the position trajectory matrix X.

Atom_1x Atom_1y Atom_1z Atom_2x Atom_2y Atom_2z …….. Atom_Nx Atom_Ny Atom_Nz
Step_1
Step_2
……
Step_M

18
The covariance matrix C is calculated using:

(11)

Where < > is the temporal average and the superscript T denotes the matrix
transpose. C is a (3N * 3N) matrix. Diagonalization of C by orthogonal transformation
produces its eigenvectors and eigenvalues:

(12)

Where U includes the eigenvectors of C as columns, and A is a diagonal matrix that

includes the eigenvalues correspond to each eigenvector in U. The eigenvector ui
(where i ranges from 1 to 3N) is called principal component. The eigenvalue ai
represents the contribution of the ith eigenvector and it reflects the motion's
magnitude through ui. Each principal component represents an atomic motion mode
[58].

In a system with N atoms, there are 3N – 6 degrees of freedom for atomic vibrations
since there are 6 vibration modes corresponds to translation and rotation motions of
the center of mass and have no restoring force, so have zero or very small frequency.
All the atomic motions are combination of these 3N – 6 normal modes [19]. To
produce 3N – 6 modes using PCA, the simulation steps M should be larger than or
equals to 3N. The last 6 eigenvalues will be zero.

Modes are sorted descendingly according to their variance such that the modes of
largest amplitudes usually come in the first few principal components [58].

4.2 Filtering the motions

The complexity of analyzing the atomic motion comes from the fact that it is a
combination of many local and global (collective) vibrational modes which make it
difficult to analyze what is happening for each of these modes throughout the
simulation time under different conditions. PCA provides a tool that filters the global
collective motions to analyze them [58].

To investigate the motion's nature of a given eigenvector ui, the trajectory matrix X is
projected on the desired eigenvector ui:

(13)

Where, pi is M dimensional vector. This projection can be used to recover the atomic
Cartesian coordinates that present only the motion of ui as following:

19
 (14)

Where, Ri is (M * 3N) matrix in which atoms are only moving based on the
vibrational mode ui.

Each Ri represents only one vibrational mode with one frequency. The magnitude of
Ri is decreasing as the i increase because PCA orders the eigenvectors such that the
highest magnitude mode is the first principal component. Each Ri can be visualized
on VMD to see the atoms' animation.

4.3 Limitation of PCA

The covariance matrix C that is diagonalized to calculate the eigenvalues and

eigenvectors of the motions includes only the linear correlations between atomic
coordinates. Hence, PCA has the capability to capture only the linear motions. If the
simulated material includes nonlinear motions, they will be neglected [58]. However,
graphene has linear and nonlinear vibrational behavior [59, 60] which means that
PCA will capture only the linear part of its motion. Gur et al [14] applied PCA to study
protein motions. Prathamesh et al [61] used PCA to analyze atomic motions of
carbon nanotube.

Many dimensionality reduction techniques other than PCA can capture the nonlinear
motions of atoms. Isomap is one of these techniques that can transform high
dimensional nonlinear data into low dimensional one that preserve most of the
topology details [62]. Tapia et al [63] applied PCA and Isomap to study the linear and
nonlinear motions of RNA respectively.

The current implementation of this report is applying PCA to study the motions of
graphene, while in the future a nonlinear dimensionality reduction technique such as
Isomap is to be used to study the motion.

20
5 Results and discussions

As mentioned in section 3.2, the molecular dynamics simulation at every step

produces thermodynamics information such as: temperature, pressure, kinetic
energy, potential energy, and total energy. In addition, it produces position, velocity,
and force of each atom at every step. Analyzing these data provided the results in
the following three sections.

5.1 Equilibration

The aim of monitoring the equilibration is to ensure that the results of the simulation
are stable at the desired conditions and not affected by the start of the simulation
[10]. It is not possible to ensure 100% confidence of equilibration. However, the
equilibration can be monitored by checking the fluctuation of the thermodynamic
properties. These properties should fluctuate around stable averages that are
independent of the initial positions and velocities of atoms.

Figure 8 a, b, and c show the temperature, potential energy, and pressure

respectively as function of time.

(a)
Temperature (Kelvin)

400

300

200

100
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000
4
x 10 (b)
Potential energy (eV)

-1.845

-1.85

-1.855

-1.86
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000

(c)
-3600
Pressure (bars)

-3800

-4000
0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000
Time (fs)

Figure 8: Time dependent fluctuation of (a) temperature, (b) potential energy, and (c) pressure.

21
Table 2 presents the mean and standard deviation values of the temperature,
potential energy, and pressure. The mean and standard deviation values are
calculated for the last 9000 fs. The fluctuation plots show that the properties
(temperature, potential energy, and pressure) start to fluctuate around stable values
before 500 fs.

The temperature is fluctuating around 299.9 which is nearly the targeted room
temperature we try to simulate. The pressure has higher fluctuation than energy and
this is usually the case in the molecular dynamics simulations [10].

Table 2: Mean and standards deviation values of temperature, potential energy, and pressure at the
last 9000 fs.

Mean Standard deviation

Temperature (Kelvin) 299.9 5.02
Potential energy (eV) -18493.54 1.9
Pressure (kbars) -3.866 0.0209

5.2 Correlation functions and phonon density of states results

The correlation functions are used to study the vibrations of the atoms. Equation (7)
shows the method to calculate the velocity correlation function. The same equation
can be used to find the correlation of atoms positions instead of velocity. Using the
position instead of the velocity produces the displacement correlation function. As
we know the velocity is the temporal derivative of displacement. The two quantities
provide the same information except that the low frequency motions are weighted
more in the displacement correlation function while the high frequency motions are
weighted more in the velocity correlation function. Assuming that Fx and Fv are the
Fourier of the displacement and velocity correlation function respectively:

(15)

Where, ω represents the frequency [53].

Figure 9 shows the displacement correlation function. Taking the Fourier transform
of the displacement correlation function provides the frequency of atoms'
vibrations. Figure 10 presents the squared magnitude of the Fourier transform. As
shown in the figure, we have peaks at the wavenumbers 10 cm -1, 17 cm-1, 27 cm-1,
and 53 cm-1. The highest one is at 17 cm-1. In section 5.3, PCA is used to investigate
the nature of the peaks of the highest magnitudes.

22
 1

0.8
Displacement correlation function

0.6

0.4

0.2

-0.2

-0.4
0 1 2 3 4 5 6 7 8 9 10
Time (ps)

Figure 9: Diplacement correlation function.

5
x 10
5

4.5

3.5

3
Intensity

2.5

1.5

0.5

0
0 50 100 150 200 250 300 350
-
wavevector (cm 1)

Figure 10: Fourier transform of displacement correlation function.

Figure 11 shows the velocity correlation function of the first 5 ps. The square
magnitude of its Fourier transform is shown in Figure 12.

23
 1

0.8

0.6
Velocity correlation function

0.4

0.2

-0.2

-0.4
0 0.5 1 1.5 2 2.5 3 3.5 4 4.5 5
Time (ps)

Figure 11: Velocity correlation function.

1400

1200

1000

800
Intensity

600

400

200

0
0 200 400 600 800 1000 1200 1400 1600 1800 2000
-
wavevector (cm 1)

Figure 12: Fourier transform of velocity correlation function.

We note two major peaks at 564 cm-1 and 1624 cm-1. As we can note from the
vibrations of the displacement and velocity correlation functions, the high frequency
vibrations are weighted more in the velocity correlation function. Moreover, the low
frequency motions that are clear in displacement correlation function approximately
disappeared except the wave at 53 cm-1. Calculating the Fourier transform of the
correlation function of atoms' forces produces the vibrations in Figure 13. It is clear
that the peak at 564 cm -1 disappeared while there is a peak at 1624 cm -1. It is noted
that the vibrations extracted from the atoms' forces do not highlight extra
information.

24
 8000

7000

6000

5000
Intensity

4000

3000

2000

1000

0
0 200 400 600 800 1000 1200 1400 1600 1800 2000
-
wavevector (cm 1)

Figure 13: Fourier transform of force correlation function.

5.3 PCA and nature of motions

In section 5.2 we presented the atoms' vibrations extracted by various correlation

functions. The displacement correlation function emphasizes more on the low
frequency vibrations. To investigate the nature of these vibrations, we can use PCA
which extracts the motions that have the highest amplitude. PCA produces principal
component (PC) of each vibration in the data. The projection of the extracted PCi on
the original data recovers new data that has only one vibration represented by PC i.
When the original data is atoms' positions, the recovered data will be atoms'
positions too. VMD can be used to look at the atoms motions of the recovered data.
However, when the original data is atoms' velocities or atoms' forces, the recovered
data will be velocities and forces respectively. In this case, it is not possible to check
atoms' motions directly by VMD as we do not have atoms' positions. Hence, we
depended on the literature to explain the nature of these vibrations.

Applying PCA on the atoms' positions produces eigenvectors which are called
principal components and eigenvalues correspond to each eigenvector. The
eigenvalue indicates the magnitude of the corresponding eigenvector and they are
ordered descendingly based on their eigenvalue. Figure 14 plots the eigenvalues
correspond to the first 30 eigenvectors. The total number of the eigenvectors equals
to atoms' number multiplied by three. The significant variance is focused on the few
first PCs and as we look at more PCs we note that their eigenvalues are gradually get
smaller. Hence, their effect on atoms' motions is negligible.

25
 15

10
Eigenvalue

0
0 5 10 15 20 25 30 35
Principal Component

Figure 14: Scree plot of eigenvalues against eigenvectors.

We note that the first two PCs have most of motion magnitudes. Recovering the
atoms' motion that are included in the first PC produce matrix R 1 (M * 3N) of all
atoms' positions. Calculating the displacement correlation function of R1 is shown in
Figure 15 while its vibration is presented in Figure 16. The frequency of this vibration
is 17 cm-1.

1.5

1
Displacement correlation function

0.5

-0.5

-1

-1.5
0 1 2 3 4 5 6 7 8 9 10
Time (ps)

Figure 15: Diplacement correlation function of R1.

26
 7
x 10
2.5

1.5
Intensity

0.5

0
0 20 40 60 80 100 120 140 160 180
-
wavevector (cm 1)

Figure 16: Fourier transform of displacement correlation function of R1.

The animation of R1 on VMD shows that this vibration represents a breathing

motion. The atoms move collectively in a direction perpendicular to the graphene
sheet.

Similarly, applying the same calculations on the second eigenvector PC 2, produces

the displacement correlation function and its Fourier transform in Figure 17 and
Figure 18 respectively. The peak in case of PC2 is at 10 cm-1. The animation of R2, the
matrix recovered based on PC2, on VMD shows also breathing vibration. We note
that the low frequency motions of graphene extracted by PCA represent breathing
motions. Videos of the vibrations of PC1 and PC2 are in the animated gif files:
movie_PC1.gif and movie_PC2.gif while the animation of the original data is in
movie_all.gif.

27
 1.5

1
Displacement correlation function

0.5

-0.5

-1

-1.5
0 1 2 3 4 5 6 7 8 9 10
Time (ps)

Figure 17: Diplacement correlation function of R2.

6
x 10
15

10
Intensity

0
0 20 40 60 80 100 120 140 160 180
wavevector (cm-1)

Figure 18: Fourier transform of displacement correlation function of R 2.

The vibrations extracted from the velocity correlation functions are at 564 cm -1 and
1624 cm-1 which imply that the phonons' energies approximately equal 0.07 eV and
0.2 eV respectively. From Figure 7 we note that the peak 0.2 eV represents the
density of states of LO and TO branches. Based on A. Jorio et al [19], the Raman
spectra of all sp2 carbon systems have G band at around 1580 cm -1 which rises TO
and LO branches. These branches are related to C-C bond stretching.

From Figure 7, we note that the peak at approximately 0.1 eV represents phonon
density of states mixed of many phonon branches. According to Nika et al [64], a
simulation that used optimized REBO potential calculated the ZA branch at K point to

28
be approximately 585 cm-1. ZA is out of plane transverse mode which reflects bond
bending interactions [56]. To clarify the positions of the two peaks of our calculation
of velocity correlation function in comparison with their equivalent vibrations in
Figure 7, we named the vibrations around peak 564 cm-1 as band A and the
vibrations around peak 1624 cm-1 as band B. Figure 19 highlights the positions of
these two bands on top of part b of Figure 7.

Band B

Band A

Figure 19: Highliting the positions of peak 564 cm-1 (Band A) and peak 1624 cm-1 (Band B) in
comparision to the equivalent vibrations of reference [56].

29
6 Conclusion and future work

In this report we have used molecular dynamics simulation and dimension reduction
technique to study vibrations of graphene. We have reviewed structure, properties,
and applications of graphene. Vacancy lattice defect and its effect on graphene
properties have been briefly discussed. We have discussed some aspects of
molecular dynamics simulations such as potential functions, ensembles, and time
step and we have presented the settings we used in our simulation. Lammps was
used to conduct the simulation. Equations of calculating correlation functions and
Fourier transform have been explained. We have depicted the application of PCA to
extract vibrations of specific magnitude and frequency and then produce atomic
coordinate trajectory that carries atomic vibration of specific mode to visualize that
vibration. The results we have produced from the simulation are presented in the
contributions section.

6.1 Contributions

Our simulation was conducted on perfect graphene sheet that is composed of 2508
atoms in the room temperature.

Applying Fourier transformation of correlation function on atoms' positions and

velocities highlights different areas of vibrational spectra. Low frequency vibrations
are weighted more in displacement correlation function while high frequency
vibrations are weighted more in velocity correlation function. Considering this fact,
we have extracted the low and high frequency vibrations from the displacement and
velocity correlation functions respectively.

The vibrational spectra of displacement correlation function revealed many peaks;

two of these peaks have the highest intensities. These two peaks are at 17 cm -1 and
10 cm-1. We have used PCA to visualize the nature of these peaks. Using PCA, we
have filtered the atoms' vibrations such that every vibration with a specific
frequency is represented alone in the atoms trajectory and visualized via VMD.
Based on the visualization, the nature of these two vibrations is like a breathing
motion.

The vibrational spectra of velocity correlation function provide two main peaks at
564 cm-1 and 1624 cm-1. The first peak 564 cm-1 corresponds to phonons that have
energy equals to 0.07 eV. Figure 19 shows the positions of the two peaks in
comparison to their equivalent vibrations published at [56]. All the sp2 carbon
systems have a peak at 1580 cm-1. This peak is related to C-C bond stretching. The

30
 peak in our results (1624 cm-1) is accurate to within less than 50 cm-1 of its
experimental position.

6.2 Future work

In the future work we intend to simulate different patterns of vacancy defects in

graphene and explore their effect on the low and high frequency vibrations. Even
and odd vacancy defects affect the properties of graphene in different manner. We
are interested to study this effect.

The related published work about graphene vibrations will be reviewed and
compared to our results.

PCA has high efficiency to extract linear motions, however, graphene motions consist
of linear and nonlinear vibrations. We plan to use a dimension reduction technique
that can capture the nonlinear motions such as Isomap.

Table 1 shows a proposed time plan of the future work required to complete this
research.

Table 3: Time plan of the future work

Tasks Months
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
1 - To study Isomap and
use it to extract
nonlinear vibrations
2 – To apply different
odd and even vacancy
defects on graphene
3 – To review graphene
vibrations from the
related published work
4 – To write the PhD
thesis

31
Bibliography

[1] A. Geim and K. Novoselov, "The rise of graphene," Nature Materials, vol. 6, no.
3, p. 183–191, 2007.

[2] R. Nair, P. Blake, A. Grigorenko, K. Novoselov, T. Booth, T. Stauber, N. Peres

and A. Geim, "Fine Structure Constant Defines Visual Transparency of
Graphene," Science, vol. 320, no. 5881, p. 1308, 2008.

[3] C. Lee, X. Wei, J. W. Kysar and J. Hone, "Measurement of the Elastic Properties
and Intrinsic Strength of Monolayer Graphene," Science, volume 321, vol. 321,
no. 5887, p. 385–388, 2008.

[4] E. Pop, V. Varshney and A. K. Roy, "Thermal properties of graphene:

Fundamentals and applications," MRS Bulletin, vol. 37, no. 12, pp. 1273-1281,
2012.

[5] W. Oswald and Z. Wu, "Energy gaps in graphene nanomeshes," Physical

Review B, vol. 85, no. 11, pp. 115431/1-115431/5, 2012.

[6] A. Balandin, S. Ghosh, W. Bao, I. Calizo, D. Teweldebrhan, F. Miao and C. N.

Lau, "Superior Thermal Conductivity of Single-Layer Graphene," Nano letters,
vol. 8, no. 3, pp. 902-907, 2008.

[7] Nobelprize.org., "The Nobel Prize in Physics 2010," 2010. [Online]. Available:
http://www.nobelprize.org/nobel_prizes/physics/laureates/2010/. [Accessed
18 October 2013].

[8] A. Kosevich, The Crystal Lattice: Phonons, Solitons, Dislocations, Superlattices,

Second ed., Wiley-VCH Verlag GmbH & Co. KGaA, 2005.

[9] S. Jafri, K. Carva, E. Widenkvist, T. Blom, B. Sanyal, J. Fransson, O. Eriksson, H.

Grennberg, O. Karis, R. Quinlan, B. Holloway and K. Leifer, "Conductivity
engineering of graphene by defect formation," vol. 43, no. 4, p. 045404, 2010.

[10] J. Haile, Molecular dynamics simulations: elementary methods, First ed.,

Wiley-Interscience, 1992.

[11] P. Larkin, IR and Raman spectroscopy: principles and spectral interpretation,

First ed., Elsevier Inc, 2011.

[12] Wikipedia, "Raman spectroscopy," [Online]. Available:

http://en.wikipedia.org/wiki/Raman_spectroscopy. [Accessed 26 October

32
 2013].

[13] Wikipedia, "Principal component analysis," Wikipedia, 11 December 2013.

[Online]. Available:
http://en.wikipedia.org/w/index.php?title=Principal_component_analysis&old
id=585629231. [Accessed 19 December 2013].

[14] M. Gur, E. Zomot and I. Bahar, "Global motions exhibited by proteins in micro-
to milliseconds simulations concur with anisotropic network model
predictions," The Journal of chemical physics, vol. 139, no. 12, p. 121912, 2013.

[15] S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics,"

Journal of Computational Physics, vol. 117, no. 1, pp. 1-19, 1995.

[16] A. Geim, "Graphene prehistory," Physica Scripta, vol. 2012, no. T146, p.
014003, 2012.

[17] K. Novoselov, A. Geim, S. Morozov, D. Jiang, Y. Zhang, S. Dubonos, I. Grigorieva

and A. Firsov, "Electric Field Effect in Atomically Thin Carbon Films," Science,
vol. 306, no. 5696, pp. 666-669, 2004.

[18] R. Heyrovska, "Atomic Structures of Graphene, Benzene and Methane with

Bond Lengths as Sums of the Single, Double and Resonance Bond Radii of
Carbon," arXiv preprint arXiv:0804.4086, 2008.

[19] A. Jorio, M. Dresselhaus, R. Saito and G. Dresselhaus, Raman spectroscopy in

graphene related systems, First ed., Wiley-VCH Verlag GmbH & Co. KGaA,
2011.

[20] J. Charlier, P. Eklund, J. Zhu and A. Ferrari, "Electron and Phonon Properties of
Graphene: Their Relationship with Carbon Nanotubes," in Carbon Nanotubes:
Advanced Topics in the Synthesis, Structure, Properties and Applications,
Springer Verlag, 2008, pp. 673-709.

[21] Wikipedia, "Electronic band structure," [Online]. Available:

http://en.wikipedia.org/wiki/Electronic_band_structure. [Accessed 24 October
2013].

[22] Wikipedia, "Conduction band," [Online]. Available:

http://en.wikipedia.org/wiki/Conduction_band. [Accessed 24 October 2013].

[23] Wikipedia, "Valence band," [Online]. Available:

http://en.wikipedia.org/wiki/Valence_band. [Accessed 24 October 2013].

33
[24] S. Morozov, K. Novoselov, M. Katsnelson, F. Schedin, D. C. Elias, J. Jaszczak and
A. Geim., "Giant Intrinsic Carrier Mobilities in Graphene and Its Bilayer,"
Physical Review Letters, vol. 100, no. 1, p. 016602, 2008.

[25] N. Mohanty and B. Vikas, "Graphene-based Single-Bacterium Resolution

Biodevice and DNA-Transistor – Interfacing Graphene-Derivatives with Nano
and Micro Scale Biocomponents," Nano Letters, vol. 8, no. 12, p. 4469–4476,
2008.

[26] X. M, F. D and H. N, "Perspectives and Challenges of Emerging Single-Molecule

DNA Sequencing Technologies," Small, vol. 5, no. 23, p. 2638–2649, 2009.

[27] D. Cohen-Tanugi and J. Grossman, "Water Desalination across Nanoporous

Graphene," Nano Letters, vol. 12, no. 7, p. 3602–3608, 2012.

[28] A. Hashimoto, K. Suenaga, A. Gloter, K. Urita and S. Iijima, "Direct evidence for
atomic defects in graphene layers," Nature, vol. 430, no. 7002, pp. 870-873,
2004.

[29] M. Wang, C. Yan, L. Ma, N. Hub and M. Chen, "Effect of defects on fracture
strength of graphene sheets," Computational Materials Science, vol. 54, pp.
236-239, 2012.

[30] F. Banhart, J. Kotakoski and A. V. Krasheninnikov, "Structural defects in

graphene," ACS nano, vol. 5, no. 1, pp. 26-41, 2010.

[31] P. Venezuela, M. Lazzeri and F. Mauri, "Theory of double-resonant Raman

spectra in graphene: Intensity and line shape of defect-induced and two-
phonon bands," Physical Review B, vol. 84, no. 3, p. 035433, 2011.

[32] V. Popov, L. Henrard and P. Lambin, "Resonant Raman spectra of graphene

with point defects," Carbon, vol. 47, no. 10, pp. 2448-2455, 2009.

[33] R. Jack, D. Sen and M. Buehler, "Graphene Nanocutting Through

Nanopatterned Vacancy Defects," Journal of Computational and Theoretical
Nanoscience, vol. 7, no. 2, pp. 354-359, 2010.

[34] A. Leach, Molecular Modelling: Principles and Applications, Second ed.,

Pearson Education Limited, 2001.

[35] N. M. Uddin, "Modeling and Simulations of Carbon Nanotube (CNT) Dispersion

in Water/Surfactant/Polymer Systems," PhD, Drexel University, 2010.

34
[36] J. E. Jones, "On the determination of molecular fields. II. From the equation of
state of a gas," Proceedings of the Royal Society of London. Series A, Containing
Papers of a Mathematical and Physical Character, vol. 106, no. 738, pp. 463-
477, 1924.

[37] S. J. Stuart, A. B. Tutein and J. A. Harrisonc, "A reactive potential for

hydrocarbons with intermolecular interactions," JOURNAL OF CHEMICAL
PHYSICS, vol. 112, no. 14, pp. 6472-6486, 2000.

[38] L. Lindsay and a. D. A. Broido, "Optimized Tersoff and Brenner empirical

potential parameters for lattice dynamics and phonon thermal transport in
carbon nanotubes and graphene," Physical Review B, vol. 81, no. 20, p.
205441, 2010.

[39] O. Lehtinen, S. Kurasch, A. V. Krasheninnikov and U. Kaiser, "Atomic scale

study of the life cycle of a dislocation in graphene from birth to annihilation,"
Nature communications, vol. 4, no. 2098, 2013.

[40] S. Y. Kim and a. H. S. Park, "The importance of edge effects on the intrinsic loss
mechanisms of graphene nanoresonators," Nano letters, vol. 9, no. 3, pp. 969-
974, 2009.

[41] J.-W. Jiang, B.-S. Wang, H. S. Park and T. Rabczuk, "Adsorbate Migration Effects
on Continuous and Discontinuous Temperature-Dependent Transitions in the
Quality Factors of Graphene Nanoresonators," Materials Science, condensed
matter. arXiv preprint arXiv:1308.3944, 2013.

[42] S. L. Roux and V. Petkov, "Model Box Periodic Boundary Conditions," Central
Michigan University, I.S.A.A.C.S. program, [Online]. Available:
http://isaacs.sourceforge.net/phys/pbc.html. [Accessed 29 October 2013].

[43] M. E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, First

ed., New York: Oxford University Press Inc., 2010.

[44] D. Evans and B. L. Holian, "The nose–hoover thermostat," The Journal of

chemical physics, vol. 83, p. 4069, 1985.

[45] B. Leimkuhler, E. Noorizadeh and F. Theil, "A gentle stochastic thermostat for
molecular dynamics," Journal of Statistical Physics, vol. 135, no. 2, pp. 261-277,
2009.

[46] M. Petyt, Introduction to finite element vibration analysis, Cambridge

35
 University Press, 2010.

[47] K. Mylvaganam and L. C. Zhang, "Important issues in a molecular dynamics

simulation for characterising the mechanical properties of carbon nanotubes,"
Carbon, vol. 42, no. 10, pp. 2025-2032, 2004.

[48] H. Zhao and N. R. Aluru, "Temperature and strain-rate dependent fracture

strength of graphene," Journal of Applied Physics, vol. 108, no. 6, pp. 064321-
064321, 2010.

[49] W. Humphrey, A. Dalke and K. Schulten, "VMD - Visual Molecular Dynamics,"

Journal of Molecular Graphics, vol. 14, pp. 33-38, 1996.

[50] "What is VMD?," Beckman Institute for Advanced Science and Technology //
National Institutes of Health // National Science Foundation // Physics,
Computer Science, and Biophysics at University of Illinois at Urbana-
Champaign., 8 April 2008. [Online]. Available:
http://www.ks.uiuc.edu/Research/vmd/allversions/what_is_vmd.html.
[Accessed 1 November 2013].

[51] J.-P. Hansen and I. R. McDonald, Theory of Simple Liquids, Third ed., Academic
Press, Elsevier Inc, 2006.

[52] J. Ramírez, S. K. Sukumaran, B. Vorselaars and A. E. Likhtman, "Efficient on the

fly calculation of time correlation functions in computer simulations," The
Journal of Cemical Physics, vol. 133, no. 154103, pp. 1-12, 2010.

[53] P. Jurgen and F. Jähnig, "Collective vibrations of an alpha-helix. A molecular

dynamics study," Biophysical journal, vol. 59, no. 4, pp. 795-804, 1991.

[54] Wikipedia, "Sine and cosine transforms," [Online]. Available:

http://en.wikipedia.org/w/index.php?title=Sine_and_cosine_transforms&oldi
d=582603136. [Accessed 8 January 2014 ].

[55] Wikipedia, "Discrete Fourier transform," [Online]. Available:

http://en.wikipedia.org/w/index.php?title=Discrete_Fourier_transform&oldid
=588438570. [Accessed 8 January 2014].

[56] G. D. Sanders, A. R. T. Nugraha, K. Sato, J.-H. Kim, J. Kono, R. Saito and C. J.

Stanton, "Theory of coherent phonons in carbon nanotubes and graphene
nanoribbons," Journal of Physics: Condensed Matter, vol. 25, p. 144201, 2013.

[57] B. C. Stipe, M. A. Rezaei and W. Ho, "Single-Molecule Vibrational Spectroscopy

36
 and Microscopy," Science, vol. 280, no. 5370, pp. 1732-1735, 1998.

[58] S. Hayward and B. L. d. Groot, "Normal modes and essential dynamics," in

Molecular Modeling of Proteins, Humana Press, 2008, pp. 89-106.

[59] L. Shen, H.-S. Shen and C.-L. Zhang, "Nonlocal plate model for nonlinear
vibration of single layer graphene sheets in thermal environments,"
Computational Materials Science, vol. 48, no. 3, p. 680–685, 2010.

[60] E. Jomehzadeh and A. Saidi, "A study on large amplitude vibration of

multilayered graphene sheets," Computational Materials Science, vol. 50, no.
3, p. 1043–1051, 2011.

[61] P. M. Shenai, Z. Xu and Y. Zhao, "Applications of Principal Component Analysis

(PCA) in Materials Science, Principal Component Analysis - Engineering
Applications," InTech, 2012.

[62] Tenenbaum, B. Joshua, V. D. Silva and J. C. Langford, "A global geometric

framework for nonlinear dimensionality reduction," Science , vol. 290.5500,
pp. 2319-2323, 2000.

[63] L. Tapia, S. Thomas and N. M. Amato, "Using dimensionality reduction to

better capture RNA and protein folding motions," Computer Science, Texas
A&M University, Texas, 2008.

[64] D. Nika and A. A. Balandin, "Two-dimensional phonon transport in graphene,"

Journal of Physics: Condensed Matter, vol. 24, no. 23, p. 233203, 2012.

[65] N. Panahi and R. Berry, "Principal component analysis of potential energy

surfaces of large clusters: allowing the practical calculation of the master
equation," Physical Chemistry Chemical Physics, vol. 11, no. 48, pp. 11638-
11646, 2009.

[66] E. Lewars, Computational chemistry: Introduction to the Theory and

Applications of Molecular and Quantum Mechanics, Second ed., Springer,
2011.

[67] P. Heino, "Dispersion and thermal resistivity in silicon nanofilms by molecular

dynamics," The European Physical Journal B, vol. 60, p. 171–179, 2007.

[68] S. K. Gupta, S. Sahoo, P. K. Jha, A. A. K. and A. Y. M., "Low Frequency Raman

Scattering from Acoustic Phonon Confined in $ CdS_ {1-x} Se_x $ Nanoparticles
in Borosilicate Glass," arXiv preprint arXiv:0803.1049, vol. , 2008.

37
[69] L. Saviot and D. B. Murray, "Longitudinal versus transverse spheroidal
vibrational modes of an elastic sphere," Physical Review B, vol. 72, no. 20, p.
205433, 2005.

38