Molecular Dynamics Studies on Nanoscale Confined Liquids

182 Pages·2017·7.82 MB·English

by  Alper Celebi

SSoouutthheerrnn MMeetthhooddiisstt UUnniivveerrssiittyy
SSMMUU SScchhoollaarr
Mechanical Engineering Research Theses and
Mechanical Engineering
Dissertations
Fall 2018
MMoolleeccuullaarr DDyynnaammiiccss SSttuuddiieess oonn NNaannoossccaallee CCoonnfifinneedd LLiiqquuiiddss
Alper Celebi
Southern Methodist University, [email protected]
Follow this and additional works at: https://scholar.smu.edu/engineering_mechanical_etds
Part of the Other Mechanical Engineering Commons, and the Transport Phenomena Commons
RReeccoommmmeennddeedd CCiittaattiioonn
Celebi, Alper, "Molecular Dynamics Studies on Nanoscale Confined Liquids" (2018). Mechanical
Engineering Research Theses and Dissertations. 14.
https://scholar.smu.edu/engineering_mechanical_etds/14
This Thesis is brought to you for free and open access by the Mechanical Engineering at SMU Scholar. It has been
accepted for inclusion in Mechanical Engineering Research Theses and Dissertations by an authorized
administrator of SMU Scholar. For more information, please visit http://digitalrepository.smu.edu.
MOLECULAR DYNAMICS STUDIES ON NANOSCALE CONFINED LIQUIDS

Approved by:

_______________________________________
Prof. Ali Beşkök
Professor in Mechanical Engineering

___________________________________
Prof. MinJun Kim
Professor in Mechanical Engineering

___________________________________
Prof. Wei Tong
Professor in Mechanical Engineering

___________________________________
Prof. Xin-Lin Gao
Professor in Mechanical Engineering

___________________________________
Prof. Vladimir Ajaev
Professor in Mathematics
MOLECULAR DYNAMICS STUDIES ON NANOSCALE CONFINED LIQUIDS

A Dissertation Presented to the Graduate Faculty of
Bobby B. Lyle School of Engineering
Southern Methodist University
in
Partial Fulfillment of the Requirements
for the degree of
Doctor of Philosophy
with a
Major in Mechanical Engineering
by
Alper Tunga Çelebi
(B.S., Istanbul Technical University, Mechanical Engineering, 2011)
(M.S., Istanbul Technical University, Mechanical Engineering, 2013)

December 15, 2018
Copyright (2018)
Alper Tunga Çelebi
All Rights Reserved
ACKNOWLEDGMENTS

I would like to express my utmost gratitude and give sincere thanks to my dissertation
advisor Prof. Ali Beşkök, for his continuous support in guiding me through my research as well
as his mentoring, encouragements and his friendship during this past a couple of years in my life.
He always has been supportive in my all academic and non-academic endeavors. This thesis
would not have been possible without his patience and attention to my studies. Furthermore,
without him, I would not have had the chance to meet exceptional people that I have met through
my graduate years. I also would like to thank my advisory committee members, Professors Xin-
Lin Gao, MinJun Kim, Wei Tong, Vladimir Ajaev for their contributions in this dissertation.
Additionally, I would like to specially thanks to Prof. Murat Barışık for his guidance and
friendship, with whom I worked closely and frequently shared ideas and discussed about our
common research interests. He became a good role model as a fellow scientist, mentor and
professor. I am also grateful for many invaluable help and support of our current and past group
members namely Amin Mansooifar, Anil Köklü, Can Sabuncu, Chinh Nguyen, Jafar Ghorbanian
and Yigit Akkus. I also would like to thank Center for Scientific Computation at Southern
Methodist University where all computations were carried out using their high-performance
computing facilities.
Finally, A special thanks to my family without their love and support this dissertation
would not exist.
iv
Çelebi, Alper Tunga B.Sc., Istanbul Technical University, Turkey, 2011
M.Sc., Istanbul Technical University, Turkey, 2013
Molecular Dynamics Studies on Nanoscale Confined Liquids

Advisor: Professor Ali Beşkök
Doctor of Philosophy in Mechanical Engineering degree conferred December 15, 2018
Dissertation completed October 25, 2018
Liquid transport in nanochannels have been attracting great interests, especially for last
two decades, owing to its potential applicability in various fields including biochemistry, medical
science and engineering. For exploring and generating new ideas in the field of nanofluidics,
molecular simulation techniques have become an ideal way due to the experimental challenges
impeding the field of nanofluidics in fabrication and measurements.
In this dissertation, we perform molecular dynamics simulations to investigate liquid
transport behavior in nanoscale channels. The expanse of this dissertation concerns several
fundamental topics in nanoscale liquid transport phenomena such as liquid properties in
nanoscale confinements, interfacial flows and slippage of fluids at the solid interface,
electrokinetic transport phenomena, and limits of continuum solutions along with developing
continuum models. Our objectives are to systematically investigate the effects of several physical
variables such as channel size, wall curvature, surface charge, salt ions, liquid-wall interfacial
strength and driving force on the nanoconfined liquid behavior. Specifically, we examine the
variations of density distributions, molecular orientations, velocity profiles, viscosities, slip
lengths and flow rates, and identify the deviations from well-known continuum bulk properties at
predefined thermodynamic state. Furthermore, we develop continuum-based analytical solutions
with slip corrections for electroosmotic flows that accurately predict transport in nanochannels.
v
TABLE OF CONTENTS

ACKNOWLEDGMENTS ......................................................................................................... iv
TABLE OF CONTENTS ........................................................................................................... vi
LIST OF FIGURES .................................................................................................................... x
LIST OF TABLES ................................................................................................................... xiv
CHAPTER 1: INTRODUCTION ............................................................................................... 1
1.1 Nanofluidics ...................................................................................................................... 1
1.2 Fluid Flow in Nanochannels ............................................................................................. 2
CHAPTER 2: MOLECULAR DYNAMICS SIMULATIONS ................................................ 11
2.1 Historical Background .................................................................................................... 11
2.2 Fundamentals of Molecular Dynamics ........................................................................... 13
2.3 Statistical Mechanics and Thermodynamic Ensembles .................................................. 15
2.3.1 Microcanonical Ensemble (NVE) ....................................................................... 16
2.3.2 Canonical Ensemble (NVT) ................................................................................ 17
2.3.3 Isothermal and Isobaric Ensemble (NPT) ........................................................... 18
2.3.4 Grandcanonical Ensemble (µVT) ........................................................................ 18
2.4 Initialization .................................................................................................................... 20
vi
2.5 Empirical Potential Functions in MD simulations .......................................................... 20
2.5.1 Bonded Potentials ................................................................................................ 22
2.5.2 Non-bonded Potentials ........................................................................................ 23
2.6 Integrating Equations of Motion ..................................................................................... 29
2.6.1 Time-integration Algorithms ............................................................................... 31
2.7 Periodic Boundary Conditions ........................................................................................ 33
2.8 Data Collecting and Statistical Averaging ...................................................................... 35
CHAPTER 3: SIZE EFFECT ON HYDRODYNAMIC SLIP LENGTH OF WATER IN
CARBON-BASED NANOCONFINEMENTS ........................................................................ 39
3.1 Introduction ..................................................................................................................... 39
3.2 Theoretical Background .................................................................................................. 41
3.3 Molecular Dynamics Simulation Details ........................................................................ 44
3.4 Force-Driven Water Flow Simulation in Periodic Domain ............................................ 45
3.5 Force-Driven Water Flow Simulations in Nanochannels ............................................... 49
3.6 Conclusion ...................................................................................................................... 58
CHAPTER 4: ELECTRIC FIELD CONTROLLED TRANSPORT OF WATER IN
GRAPHENE NANOCHANNELS ........................................................................................... 60
4.1 Introduction ..................................................................................................................... 60
4.2 Theoretical Background .................................................................................................. 62
4.3 Molecular Dynamics Simulation Details ........................................................................ 64
vii
4.4 Results ............................................................................................................................. 69
4.5 Conclusion ...................................................................................................................... 89
CHAPTER 5: SURFACE CHARGE DEPENDENT TRANSPORT OF WATER IN
GRAPHENE NANOCHANNELS ........................................................................................... 90
5.1 Introduction ..................................................................................................................... 90
5.2 Theoretical Background .................................................................................................. 93
5.3 Molecular Dynamics Simulation Details ........................................................................ 93
5.4 Results ............................................................................................................................. 98
5.5 Conclusion .................................................................................................................... 107
CHAPTER 6: MOLECULAR AND CONTINUUM TRANSPORT PERSPECTIVES ON
ELECTROOSMOTIC SLIP FLOWS ..................................................................................... 110
6.1 Introduction ................................................................................................................... 110
6.2 Theoretical Background: Governing Equations in Electrokinetic Theory ................... 114
6.2.1 Poisson’s Equation ............................................................................................ 115
6.2.2 Navier-Stokes Equations ................................................................................... 121
6.2.3 Prediction of Surface Charge Density and Zeta Potential ................................. 124
6.3 Molecular Dynamics Simulation Details ...................................................................... 127
6.4 Results ........................................................................................................................... 132
6.4.1 Equilibrium Simulations .................................................................................... 135
6.4.2 Force-Driven Flow Simulations ........................................................................ 137
viii
6.4.3 Electroosmotic Flow Simulations ..................................................................... 139
6.5 Conclusion .................................................................................................................... 145
CHAPTER 7: SUMMARY AND FUTURE RESEARCH .................................................... 148
7.1 Summary of the Current Work ..................................................................................... 148
7.2 Future Research ............................................................................................................ 150
BIBLIOGRAPHY ................................................................................................................... 152

ix