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Computational Nanotechnology Modeling and
Applications with MATLAB R Sarhan M Musa Digital
Instant Download
Author(s): Sarhan M Musa
ISBN(s): 9781439841778, 1439841772
Edition: ebook
File Details: PDF, 45.64 MB
Year: 2012
Language: english
Computational
Nanotechnology
Modeling and
Applications
with MATLAB®
 Nano and Energy Series
Series Editor: Sohail Anwar

Computational Nanotechnology: Modeling and Applications with MATLAB®

Sarhan M. Musa

Forthcoming titles
Sustainable Manufacturing
Arun N. Nambiar and Adnar H. Sabuwala
Nanotechnology: Business Applications and Commercialization
Sherron Sparks
Green Building: Applied Nanotechnology and Renewable Energy
Sohail Anwar
Advanced Nanoelectronics
Razali Bin Ismail, Mohammad Taghi Ahmadi, and Sohail Anwar
Nanotechnology: Social and Ethical Issues
Ahmed S. Khan
Introduction to Renewable Energy Systems
Sohail Anwar
Edited by
Sarhan M. Musa
MATLAB® is a trademark of The MathWorks, Inc. and is used with permission. The MathWorks does not warrant the
accuracy of the text or exercises in this book. This book’s use or discussion of MATLAB® software or related products
does not constitute endorsement or sponsorship by The MathWorks of a particular pedagogical approach or particular
use of the MATLAB® software.

CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742
© 2012 by Taylor & Francis Group, LLC
CRC Press is an imprint of Taylor & Francis Group, an Informa business

No claim to original U.S. Government works

Version Date: 20110808

International Standard Book Number-13: 978-1-4398-4177-8 (eBook - PDF)

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 To my father Mahmoud,

my mother Fatmeh, and my wife Lama

Contents

Preface...............................................................................................................................................ix
Acknowledgments...................................................................................................................... xvii
Editor............................................................................................................................................. xix
Contributors.................................................................................................................................. xxi

1. Introduction to Computational Methods in Nanotechnology....................................... 1

Orion Ciftja and Sarhan M. Musa

2. Computational Modeling of Nanoparticles..................................................................... 29

Ufana Riaz and S.M. Ashraf

3. Micromagnetics: Finite Element Analysis of Nano-Sized Magnetic Materials

Using MATLAB®................................................................................................................... 75
Shin-Liang Chin and Timothy Flack

4. System-Level Modeling of N/MEMS................................................................................ 97

Jason Vaughn Clark

5. Numerical Integrator for Continuum Equations of Surface

Growth and Erosion.......................................................................................................... 189
Adrian Keller, Stefan Facsko, and Rodolfo Cuerno

6. Configuration Optimizations and Photophysics Simulations of Single-Wall

Nanotubes of Carbon, Silicon-Carbide, and Carbon-Nitride.................................... 217
W.-D. Cheng, C.-S. Lin, G.-L. Chai, and S.-P. Huang

7. MATLAB® Applications in Behavior Analysis of Systems Consisting

of Carbon Nanotubes through Molecular Dynamics Simulation............................. 251
Masumeh Foroutan and Sepideh Khoee

8. Device and Circuit Modeling of Nano-CMOS.............................................................. 301

Michael L.P. Tan, Desmond C.Y. Chek, and Vijay K. Arora

9. Computational and Experimental Approaches to Cellular and Subcellular

Tracking at the Nanoscale.................................................................................................. 333
Zeinab Al-Rekabi, Dominique Tremblay, Kristina Haase, Richard L. Leask,
and Andrew E. Pelling

10. Computational Simulations of Nanoindentation and Nanoscratch......................... 363

Cheng-Da Wu, Te-Hua Fang, and Jen-Fin Lin

11. Modeling of Reversible Protein Conjugation on Nanoscale Surface....................... 381

Kazushige Yokoyama

vii
viii Contents

12. Computational Technology in Nanomedicine.............................................................. 411

Viroj Wiwanitkit

13. Future Directions: Opportunities and Challenges...................................................... 429

George C. Giakos

Appendix A: Material and Physical Constants................................................................... 451

Appendix B: Symbols and Formulas..................................................................................... 455
Appendix C: MATLAB®........................................................................................................... 471
Preface

Nanotechnology and nanoscience have now emerged as the leading fields to a techno-
logical revolution in the new millennium. Nanotechnology involves research across dis-
ciplines such as engineering, physics, chemistry, biology, and medicine. It engages in
the science of matter that is smaller than 100 nm. Therefore, the ability to manipulate
atoms at the nanoscale helps scientists create tiny devices the size of a few atoms for many
applications such as consumer supplies, electronics, and computers in the development of
molecular-sized transistors for the memory of microcomputers, as well as in the fields of
information and biotechnology, aerospace, energy, and environment, and in the improve-
ment of drug delivery in identifying cancer cells in medicine, in energy productions, etc.
Using nanotechnology brings many benefits to industry as it requires little labor and low
cost. This book can be used as a reference by engineers, scientists, and biologists who are
involved in the computational techniques of nanotechnology. It has been written for pro-
fessionals, researchers, and students who need to discover the challenges and the oppor-
tunities concerning the development of the next generation of nanoscale computational
nanotechnology: modeling and applications with MATLAB®. It provides a broad spectrum
of technical information, research ideas, and practical knowledge regarding nanotechnol-
ogy applications, and intends to provide a thought-provoking perspective on how nano-
technology is poised to revolutionize the field of computational nanotechnology. It also
describes emerging nanotechnology applications as well as nanotechnology applications
under development that hold promise for significant innovations in engineering, physics,
chemistry, biology, and medicine.
The book has been divided into 13 chapters. Chapter 1 presents an introduction to
computational methods in nanotechnology. It shows that nanoscale structures are quite
intriguing because in the nanometer region almost all physical and chemical properties
of systems are generally size dependent. The dependence on size of properties of such
materials makes them fascinating from a technological and theoretical point of view. At
the same time, nanoscale science and engineering offers an entirely new design motif
for developing advanced materials and new devices. The nanoscience revolution has
created an urgent need for a more robust quantitative understanding of matter at the
nanoscale through modeling and simulation. Realizing this potential, however, will
require a concerted effort in theoretical and modeling research to overcome some of the
computational challenges in the field. Because of the variety and large number of nanoscale
building blocks, it is impossible to cover all of them here. However, we will try to give a
brief overview of two very important nanoscale systems—molecular magnets and semi-
conductor quantum dots. The objective of Chapter 1 is to look closely at the theory and
modeling of these two nanoscale systems and also to briefly address some of the critical
research issues in the fast-evolving field of nano-magnetism and nano-electronics, where
molecular magnets and quantum dots are the respective building blocks. Studies of
molecular magnets and semiconductor quantum dots offer great promise for the future
technologies, but demand computationally intensive work. In order to get the fullest
understanding of the basic properties of various nanoscale systems, a wide range of mul-
tidisciplinary scientists is required in order to utilize various modeling approaches and
tools including MATLAB. While focusing on specific examples of ultrasmall systems, we
attempt to give a brief and basic understanding of various computational methods that

ix
x Preface

help us to understand the key properties of various nanoscale molecular magnetic and
semiconductor quantum dot systems.
Chapter 2 presents computational modeling of nanoparticles. Nanomaterials constitute
an emerging subdiscipline in the chemical and materials sciences. All conventional mate-
rials like metals, semiconductors, glass, ceramic, or polymers can in principle be obtained
with a nanoscale dimension. Nanomaterials have various microstructural features such
as nanodiscs, quantum dots, nanowires, nanotubes, nanocoatings, and nanocomposites.
The unique functionality of nanoparticle-based materials and devices depends directly
on size- and structure-dependent properties. Nanoparticle size must be tightly controlled
to take full advantage of quantum size effects in technological applications, and agglom-
eration must be prevented. This can only be done if the concentration is controlled, which
requires that the rate of new particle formation be quantitatively determined. Real-time
measurements of particle size distributions and particle structure are, thus, enabling
techniques for the advancement of nanotechnology. Accurate and reliable models for
simulating transport, deposition, coagulation, and dispersion of nanoparticles and their
aggregates are needed for the development of design tools for technological applica-
tions, including nanoparticle instrumentation, sampling, sensing, dilution, and focusing
nanoparticle behavior in chemically reactive systems.
Computational techniques allow us to explore and validate hypotheses about experi-
mentally observed behavior that may otherwise not be accessible through traditional
experimental techniques. Additionally, computer simulations allow for theory to propose
areas of interest to which experimental techniques may be applied. Two of the most com-
mon computer simulation methods, Monte Carlo (MC) and molecular dynamics (MD),
have been widely applied to a variety of model systems ranging from large proteins to
nanoclusters. Computer science offers more opportunities for nanotechnology. Soft com-
puting techniques such as swarm intelligence, genetic algorithms, and cellular automata
can impart desirable emergent properties like growth, self-repair, and complex networks
to systems. Many researchers have successfully applied such techniques to real-world
problems, including complex control systems in manufacturing plants and air traffic con-
trol. Research in intelligent systems involves the understanding and development of intel-
ligent computing techniques as well as the application of these techniques for real-world
tasks, often to the problems of other research areas. The techniques in intelligent systems
comprise methods or algorithms in artificial intelligence (AI), knowledge representation/
reasoning, machine learning, and natural computing or soft computing. With some modi-
fications in nanotechnology characteristics, these techniques can be applied to control a
swarm of a trillion nanoassemblers. It is anticipated that soft computing methods such as
these will overcome concerns about harmful implications of nanotechnology and prevent
the notorious scenario of self-replicating nanorobots multiplying uncontrollably.
A preliminary framework has been developed to help determine what research is
needed and how it can be integrated into the designing of computer-simulated models of
nanoparticles. The focus of Chapter 2 is to highlight the significance of nanoparticles and
the challenges in the integration of these nanomaterials for their potential applications in
various fields.
Chapter 3 presents micromagnetics: finite element analysis of nano-sized magnetic
materials using MATLAB. Fabrication techniques developed over the past decades have
allowed engineers and scientists to form magnetic materials in the nanometer regime.
Such materials exhibit very interesting magnetic properties that are significantly different
from bulk materials. At such scales, the behaviors of the magnetic materials are inade-
quately described by Maxwell’s equations alone. The theory of micromagnetics deals with
Preface xi

the behaviors of these nano-sized magnetic materials by including the quantum mechani-
cal effects that are significant at this scale. Micromagnetics theory has been successful in
predicting the formation of domain walls in magnetic materials and also the formation of
interesting magnetic states such as the vortex and leaf states. It also finds its application
in many engineering aspects such as the digital data storage technology. Chapter 3 will
introduce the basic theory of micromagnetics, show how the finite element method can be
applied to the governing equation of micromagnetics (Landau–Lifshitz–Gilbert equation),
and finally show how all these can be done using MATLAB.
Chapter 4 presents system-level modeling of N/MEMS; it discusses some of the latest
advances in designing and modeling complex nano- and microelectromechanical (N/MEMS)
systems at the system level. These advances have been applied to an open source tool called
PSugar at Purdue University. For design, the author discusses a graphical user interface (GUI)
that allows users to quickly configure complex systems in 3D using a computer mouse or pen
at a rate faster than what might be drawn with pencil and paper. This GUI is coupled to a
powerful net list language for design flexibility.
For modeling, the chapter applies recent advances in analytical system dynamics and
differential–algebraic equations (DAEs) into a framework that facilitates the systematic
modeling of multidisciplinary systems that may comprise static or dynamic constraints.
Where appropriate, we verify lumped models against their distributed model counterparts.
Several test cases are discussed that demonstrate a wide range of utility of system-level
analysis for N/MEMS. The test cases include simple to complex MEMS, and NEMS using
molecular dynamics.
Chapter 5 explains numerical integrators for continuum equations of surface growth and
erosion. Growth of thin films by physical vapor deposition and erosion of solid surfaces
by ion beam sputtering have high relevance in the fields of micro- and nanotechnology.
Therefore, the theoretical modeling of the surface morphology and its evolution during
growth and erosion have received considerable attention. Compared to atomistic models,
continuum equations are able to cover a much larger spatial and temporal scale accessing
the macroscopic scales at which nontrivial features of the morphological dynamics occur.
This is especially relevant for surface erosion, which can induce a linear instability of the
surface, resulting in the formation of periodic nanoscale patterns.
In Chapter 5, the software package “Ripples and Dots” is presented, which is designed
for the numerical integration of continuum equations modeling the surface evolution dur-
ing ion beam erosion in (2 + 1) dimensions. These equations are based on the Bradley–
Harper model and often feature, in addition to the linear instability, nonlinear and noise
terms, for example, the prominent Kuramoto–Sivashinsky equation. However, due to the
similarity with continuum equations for interface growth, the software package can be
used as well for studying continuum equations describing thin film growth, like the well-
known Kadar–Parisi–Zhang equation, the Edwards–Wilkinson equation, and the linear
molecular beam epitaxy equation.
Numerical data obtained by integrating various continuum equations for surface ero-
sion are presented and compared to analytical predictions and experimental observations.
It is demonstrated that the evolution of the surface morphology observed in the numerical
integrations is in good qualitative agreement with experimental results both for normal
and oblique ion incidence. In addition, special cases of erosion at oblique ion incidence
with simultaneous sample rotation and erosion with multiple ion beams are presented.
Chapter 6 presents configuration optimizations and photophysics simulations of single-
wall nanotubes of carbon, silicon-carbide, and carbon-nitride. First, the authors opti-
mize the structures of ground state for finite open single-wall carbon nanotubes (CNTs)
xii Preface

of (n, n) type (n = 3–6) by B3LYP/6-31G* level. They then calculate the electronic struc-
tures and simulate the electronic absorption, third-order polarizability, and two-photon
absorption spectra by TDB3LYP/6-31G* level combining with sum-over-states method
based on the optimized configurations. The obtained results show that the tube diam-
eter increases, the gap between LUMO–HOMO reduces, electronic absorption spectrum
is redshift, and two-photon absorption cross section enhances as chiral vector length
increases at constant axis length for (n, n) tubes. It is shown that the third-order polariz-
ability along with the tube-axis direction decreases, as the bisector direction between
the parallel and perpendicular to the tube axis increases while chiral vector length
of (n, n) tube increases. That is, the smaller diameter and the larger the anisotropy of
polarizabilities are for finite open single-wall CNTs with the same length of tube axes.
The π–π charge transfers within (n, n) tubes are the electronic originations of nonlin-
ear polarizability and two-photon absorption spectra at low-energy regions, in view of
state-dependent third-order polarizability and configuration interaction contributions.
Second, the authors employ periodical density functional theory to investigate geometri-
cal structures and linear optical properties of SiC and CNTs with different types. The
obtained results indicate that the optical properties of the zigzag, armchair, and chiral
SiC nanotubes are dependent on the diameter and chirality. It is indicated that the arm-
chair CNTs appear as polygons while zigzag ones are circles. Both the armchair and
zigzag CNTs are direct band gap semiconductors and their band gaps are dependent
on tube size and chirality. The calculated dielectric functions of CNTs are dependent on
tube size and the directions of polarization.
Chapter 7 explains MATLAB applications in behavior analysis of systems consisting of
CNTs through molecular dynamics simulation. This chapter presents the applications of
MATLAB in calculations for nano-systems, which mostly contain CNTs and consist of five
sections.
In Section 7.2, the molecular dynamic simulation and analytical studies of nano-oscillators
are reviewed. Also, some specialized applications of MATLAB for studying the behavior of
nano-oscillators are introduced.
In Section 7.3, the authors study the behavior of (8, 2) single-walled CNTs and function-
alized CNTs (FCNTs) with four functional groups in water using the molecular dynamic
simulation method. Glutamine, as a long chain functional group, and carboxyl, as a short
chain functional group, have been used as functional groups in FCNTs. Four functional
groups in each FCNT were localized at two positions: (i) all four functional groups were
in the sidewalls of the nanotube and (ii) two functional groups were at the ends and two
functional groups were in the sidewalls of the nanotube. The intermolecular interaction
energies between CNTs or FCNTs and water molecules, the plots of radial distribution
function, and the diffusion coefficients of CNTs and FCNTs in water were computed for
investigating the effects of type and position of functional groups on the behavior of
FCNTs in water. The obtained results from three methods are consistent with each other.
Results showed that the position of the functional groups in FCNTs has an important role
in the interaction of hydrophilic groups of FCNTs with water molecules.
Furthermore, the authors also investigated the behavior of FCNTs with 16 carboxyl func-
tional groups in water. The presence of these large numbers of carboxyl functional groups
on CNTs prevents water molecules from moving toward hydrophilic carboxyl functional
groups. This well demonstrates the advantage of using a lower number of functional
groups, each containing many hydrophilic groups like the glutamine functional group.
In Section 7.4, the molecular dynamics simulations were presented to investigate the
interfacial binding between the single-walled CNTs and conjugated polymers including
Preface xiii

polythiophene (PT), polypyrrole (PP), poly (2,6-pyridinylenevinylene-co-2,5-dioctyloxy-p-

phenylenevinylene) (PPyPV), and poly(m-phenylenevinylene-co-2,5-dioctyloxy-p-phenyl-
enevinylene) (PmPV).
The intermolecular interaction energy between single-walled CNTs and polymer mol-
ecules was computed and the morphology of polymers physisorbed to the surface of nano-
tubes was investigated by the radius of gyration and the alignment angle. The influence
of nanotube radius and temperature on the interfacial adhesion of nanotube–polymer and
Rg of polymers was explored in detail. Our simulation results showed that the strongest
interaction between the single-walled CNTs and these conjugated polymers was observed
first for PT, then for PPy and PmPV, and finally for PPyPV. Our results showed that the
intermolecular interaction in our systems is strongly influenced by the specific monomer
structure of polymer and nanotube radius, but the influence of temperature could be negli-
gible. The high values of intermolecular interaction energy of such composites suggest that
an efficient load transfer exists in the interface between nanotube and heterocyclic conju-
gated polymer, which plays a key role in composite reinforcement practical applications.
In Section 7.5, using molecular dynamics simulations, neon adsorption on an open-
ended (10, 10) single-walled CNT was investigated at supercritical temperatures of neon,
that is, T = 50, 70, and 90 K. Adsorption isotherms, heat of adsorption, self-diffusion coef-
ficients, activation energy, and structural properties of neon gas were computed and ana-
lyzed in detail. All adsorption isotherms are predicted to be of Langmuir shape type I at
this range of temperature. The results showed that the temperature is in direct correlation
with adsorption capacity, that is, increasing the temperature causes lower adsorption of
neon gas by single-walled CNTs. All aforementioned quantities confirm this fact and are
in good agreement with previous experimental and theoretical works.
Chapter 8 discusses device and circuit modeling of nano-CMOS. The mobility and satu-
ration velocity are the two important parameters that control the charge transport in a
conducting MOSFET channel. The mobility is degraded both by the gate electric field as
well as by the channel electric field, the former due to quantum-confinement and the latter
due to streamlining of velocity vectors in the intense driving electric field. The saturation
velocity in the channel is ballistic, that is, limited to the thermal velocity for nondegener-
ate carriers and to the Fermi velocity for degenerate carriers in the inversion regime. The
calculated current–voltage characteristics of a MOSFET channel in the inversion regime
using MATLAB are in agreement with the experimental data on a 45 and 80 nm channel.
Additional modeling steps can be implemented in MATLAB environment to simulate
drain current versus gate voltage and extract the drain-induced barrier lowering (DIBL),
substhreshold swing (SS), and on–off ratio. Voltage transfer curve (VTC) of a complemen-
tary transistor (p- and n-type) to extract the DC gain, noise margin, rising time, falling
time, and propagation delay via RC delay model are all easily implementable in MATLAB.
This could be an easy alternative to HSPICE where the design of a new formulation of a
transistor model is done using SPICE’s voltage-controlled current source (VCCS) subcir-
cuit. Moreover, simulation programs are unable to keep pace with the changes that are
needed as devices are scaled down to nanometer scale.
Chapter 9 covers computational and experimental approaches to cellular and subcel-
lular tracking at the nanoscale. It has been shown that the cell maintains control over its
mechanical properties and that these control mechanisms are highly influenced by the
mechanical microenvironment. Many elements of cellular control are found in the cytoar-
chitecture (cytoskeleton, focal adhesions, contractility, and the extracellular matrix). Each
of these elements contributes in some way to the transduction of mechanical information
into a biochemical signal, which allows the cell to perform the necessary physiological
xiv Preface

functions. Live cell imaging involves noninvasive analysis of dynamical processes using
confocal, epi-fluorescence, atomic force, and traction force microscopies, and the use of
computational techniques for further quantification of cellular dynamics. In this chap-
ter, we present two MATLAB codes based on particle tracking to compute traction force
fields: spatial tracking of cellular structures and cellular deformation. The chapter begins
with an overview of the main structural components of the cytoskeletons that play a pri-
mary role in the mechanical behavior of eukaryotic cells. This is followed by a description
of two types of mechanically tunable substrates available to investigate cellular traction
forces and the effect of mechanical forces on cellular behavior. We will also show how con-
focal and epi-fluorescent microscopy techniques can be used to image cellular responses
and provide images that can be analyzed using computational approaches in MATLAB.
Chapter 10 discusses computational simulations of nanoindentation and nanoscratch. It
describes molecular dynamics (MD) simulation and its uses in investigating the atomistic
mechanisms of nanoindentation and nanoscratch processes under different indentation
loads, various contact interferences, temperatures, and loading rates. The results showed
that when the loads and the loading rates increased, both Young’s modulus and the hard-
ness of the films increased. When the indentation was operating under high temperatures,
the thermal softness behavior took place causing a reduction in Young’s modulus. The
frictional and indented behavior of a diamond asperity on a diamond plate was carried
out using molecular dynamics and experiments. The contact load, contact area, dynamic
frictional force, and dynamic frictional coefficient increased as the contact interference
increased at a constant loading velocity. The contact and frictional behavior can be evalu-
ated between a rigid smooth hemisphere and a deformable rough flat plane by combining
the deformed behavior of the asperity obtained from MD results with the fractal and sta-
tistic parameters. The comparison and the discrepancy of simulated results and nanoin-
dentation and scratching experimental results have also been discussed.
Chapter 11 discusses the modeling of reversible protein conjugation on nanoscale sur-
face. The protein-coated gold nanoparticles can be used to investigate the conformational
change of proteins at a solid–liquid interface. This approach was applied to investigate
the conjugation of amyloid β protein (Aβ) over gold nanocolloid in conjunction with a
mechanism of fibrillogenesis, which is associated with Alzheimer’s disease. Among tested
Aβ proteins and various sizes of gold colloids, only Aβ1–40-coated 20 ± 1 nm gold colloidal
nanoparticles exhibited a reversible color change as the pH was externally altered between
pH 4 and 10. This size-selective reversibility is an important implication for the initial
reversible step reported for the fibrillogenesis of Aβ1–40. When the process was repeated
with ovalbumin, all tested sizes of gold colloidal nanoparticles (10, 20, 30, 40, 50, 60, 80, and
100 nm) showed a quasi-reversible color change, implying that the conjugation process
is partially dependent on the protein. Temperature-dependent features were observed
in the reversibility of Aβ1–40 conjugated to 20, 30, and 40 nm gold colloidal suspension.
While Aβ1–40-coated 20 nm gold colloid nanoparticles exhibited a reversible color change
under 50°C except for 5°C ± 0.2°C and lower, Aβ1–40-coated 30 and 40 nm colloids exhib-
ited reversible color change when the temperature was lowered to 18°C ± 0.2°C and 6°C ±
0.2°C, respectively. This specific and unique size and temperature dependence in revers-
ible color change strongly suggest that the noncovalent intrinsic intermolecular potential
formed between the nanocolloidal surface and each Aβ1–40 monomer conjugated at the
surface drives the process. Our series of studies explored conformational changes unique
to the surface size of the gold colloidal nanoparticles and opened new insights for protein-
associated nanomaterials.
Preface xv

Chapter 12 deals with computational technology in nanomedicine. It shows that, at pres-

ent, nanomedicine is an important branch of nanotechnology. It is a very useful novelty
in medicine and holds promise in the diagnosis and treatment of several diseases. The
application of computational technology plays an important role in the development of
nanomedicine research. Several computer programs can be useful in conducting research
in this field. However, an important and easy-to-use program is MATLAB, which can help
medical scientists answer complex questions. Simulation of complex biological processes
can be easily performed based on MATLAB. The author, therefore, elaborates on how
MATLAB can be useful in nanomedicine. Also, a summary of important reports on the
application of MATLAB in nanomedicine is given in this chapter.
Chapter 13 presents future directions: opportunities and challenges for computational
nanotechnology. It shows that the major research objectives in molecular nanotechnol-
ogy are the design, modeling, and fabrication of molecular microchips, instrumenta-
tion, machines, and molecular devices. The design and modeling of molecular machines
requires, however, intensive computational efforts. Efficient nanoscale systems algo-
rithms, molecular modeling software, and efficient mathematical computational tools are
of primary importance. In this chapter, the technical challenges of mathematical modeling
in the nanotechnology arena are highlighted by introducing future nanoscale systems
research directions, nanophotonics technological advances, reconfigurable and adaptable
biomolecular structures, and novel nanoscience applications that may have a significant
technological and societal impact on humanity.
Finally, the book concludes with three appendices: Appendix A shows common mate-
rial and physical constants, with the considerations that the materials constants values
varied from one published source to another due to many varieties of most materials and
also because conductivity is sensitive to temperature, impurities, and moisture content, as
well as the dependence of relative permittivity and permeability on temperature, humid-
ity, and the like; Appendix B shows common symbols and useful mathematical formulas;
Appendix C covers basic tutorial on MATLAB.

Sarhan M. Musa
Editor

For MATLAB® and Simulink® product information, please contact:

The MathWorks, Inc.

3 Apple Hill Drive
Natick, MA, 01760-2098 USA
Tel: 508-647-7000
Fax: 508-647-7001
E-mail: [email protected]
Web: www.mathworks.com
Acknowledgments

I would like to express my sincere appreciation and gratitude to all the book’s contribu-
tors. Thank you to Brain Gaskin for his wonderful heart and for being a great American
neighbor. I would also like to thank Kerry L. Madole for her support and understanding.
It is my great pleasure to acknowledge the outstanding help of the team at Taylor & Francis/
CRC Press in preparing this book, especially from Nora Konopka, Kari Budyk, Glenon C.
Butler, Jr., and Brittany Gilbert. Thanks also to Arunkumar Aranganathan from SPi Global
for his outstanding help. Many thanks to Professor Sohail Anwar for his useful comments
and Naomi Fernande for her great suggestions. I would also like to thank Dr. Kendall Harris,
my college dean, for his constant support. Finally, the book would never have seen the
light of day if not for the constant support, love, and patience of my family.

xvii
Editor

Sarhan M. Musa received his PhD in electrical ­engineering

from City University of New York, New York. He is ­currently
an associate professor in the Department of Engineering
Technology at Prairie View A&M University, Texas. He has
been director of Prairie View Networking Academy, Texas,
since 2004. From 2009 to 2010, Dr. Musa was a visiting
professor in the Department of Electrical and Computer
Engineering and also worked in the Nanoelectronic Systems
Laboratory at Rice University, Texas. His research interests
include computational methods in nanotechnology, com-
puter communication networks, and numerical modeling of
electromagnetic systems. He has published more than 100 papers in peer-reviewed jour-
nals and conferences. He currently serves on the editorial board of the Journal of Modern
Applied Science. Dr. Musa is a senior member of the Institute of Electrical and Electronics
Engineers. He is also a 2010 Boeing Welliver Fellow.

xix
Contributors

Zeinab Al-Rekabi Shin-Liang Chin

Department of Physics Cavendish Laboratory
University of Ottawa University of Cambridge
Ottawa, Ontario, Canada Cambridge, United Kingdom

Vijay K. Arora Orion Ciftja

Faculty of Electrical Engineering Department of Physics
Universiti Teknologi Malaysia Prairie View A&M University
Skudai, Malaysia Prairie View, Texas
and
Jason Vaughn Clark
Division of Engineering and Physics
School of Electrical and Computer
Wilkes University
Engineering
Wilkes-Barre, Pennsylvania
School of Mechanical Engineering
Purdue University
S.M. Ashraf West Lafayette, Indiana
Materials Research Laboratory
Department of Chemistry
Rodolfo Cuerno
Jamia Millia Islamia
Departamento de Matemáticas
New Delhi, India
Grupo Interdisciplinar de Sistemas
Complejos
G.-L. Chai Universidad Carlos III de Madrid
State Key Laboratory of Structural Leganés, Spain
Chemistry
Fujian Institute of Research on the
Stefan Facsko
Structure of Matter
Institute of Ion Beam Physics and Materials
Chinese Academy of Sciences
Research
Fuzhou, Fujian, China
Helmholtz-Zentrum Dresden-Rossendorf
Dresden, Germany
Desmond C.Y. Chek
Faculty of Electrical Engineering
Universiti Teknologi Malaysia Te-Hua Fang
Skudai, Malaysia Department of Mechanical Engineering
National Kaohsiung University of Applied
Sciences
W.-D. Cheng Kaohsiung, Taiwan
State Key Laboratory of Structural
Chemistry
Fujian Institute of Research on the Timothy Flack
Structure of Matter Department of Engineering
Chinese Academy of Sciences University of Cambridge
Fuzhou, Fujian, China Cambridge, United Kingdom

xxi
xxii Contributors

Masumeh Foroutan Richard L. Leask

Department of Physical Chemistry Department of Chemical Engineering
School of Chemistry McGill University
College of Science Montreal, Quebec, Canada
University of Tehran
Tehran, Iran C.-S. Lin
State Key Laboratory of Structural
Chemistry
George C. Giakos Fujian Institute of Research on the
Department of Electrical and Computer Structure of Matter
Engineering Chinese Academy of Sciences
The University of Akron Fuzhou, Fujian, China
Akron, Ohio
Jen-Fin Lin
Kristina Haase Department of Mechanical Engineering
Department of Physics National Cheng Kung University
University of Ottawa Tainan, Taiwan
Ottawa, Ontario, Canada
Sarhan M. Musa
Department of Engineering Technology
S.-P. Huang Prairie View A&M University
State Key Laboratory of Structural Prairie View, Texas
Chemistry
Fujian Institute of Research on the Andrew E. Pelling
Structure of Matter Department of Physics
Chinese Academy of Sciences
Fuzhou, Fujian, China and
Department of Biology
Adrian Keller University of Ottawa
Institute of Ion Beam Physics and Materials Ottawa, Ontario, Canada
Research
Helmholtz-Zentrum Dresden-Rossendorf Ufana Riaz
Dresden, Germany Materials Research Laboratory
Department of Chemistry
and Jamia Millia Islamia
Interdisciplinary Nanoscience Center New Delhi, India
Aarhus University
Aarhus, Denmark Michael L.P. Tan
Faculty of Electrical Engineering
Universiti Teknologi Malaysia
Sepideh Khoee Skudai, Malaysia
Department of Polymer Chemistry
and
School of Chemistry
College of Science Department of Engineering
University of Tehran University of Cambridge
Tehran, Iran Cambridge, United Kingdom
Contributors xxiii

Dominique Tremblay Cheng-Da Wu

Department of Physics Department of Mechanical Engineering
University of Ottawa National Kaohsiung University of Applied
Ottawa, Ontario, Canada Sciences
Kaohsiung, Taiwan
Viroj Wiwanitkit
Hainan Medical University
Haikou, Hainan, China Kazushige Yokoyama
Department of Chemistry
and The State University of New York College
Wiwanitkit House at Geneseo
Bang Khae, Bangkok, Thailand Geneseo, New York
1
Introduction to Computational Methods
in Nanotechnology

Orion Ciftja and Sarhan M. Musa

CONTENTS
1.1 Introduction............................................................................................................................. 1
1.2 Molecular Magnetism............................................................................................................ 4
1.3 Semiconductor Quantum Dots........................................................................................... 12
1.4 Conclusion.............................................................................................................................22
References........................................................................................................................................ 24

1.1 Introduction
Nanoscale science and engineering offer the possibility for revolutionary advances in both
fundamental science and technology and may have an impact on our economy and society
that is comparable in scale and scope to the transistor electronics and the Internet. At its
basic level, nanoscale science is the study of novel phenomena and properties of materials
that occur at extremely small length scales, typically on the nanoscale that is the size of
atoms and molecules [1]. On a similar path, nanotechnology is the application of nano-
science and engineering methods to produce novel materials and devices [2]. The terms
nanostructure, nanoscience, and nanotechnology are currently quite popular in both the
scientific and the general press.
Nanoscale structures are quite intriguing because generally in the nanometer region,
almost all physical and chemical properties of systems become size dependent. For exam-
ple, although the color of a piece of gold remains golden as it reduces from centimeters
to microns, the color changes substantially in the regime of nanometers. Similarly, the
melting temperatures of small systems change as they enter the nanoscale region, where
the surface energies become comparable to the bulk energies. Because properties at the
nanoscale are size dependent, nanoscale science and engineering offer an entirely new
design motif for developing advanced materials and new devices.
The nanoscience revolution has created an urgent need for a more robust quantitative
understanding of matter at the nanoscale by modeling and simulation since the absence
of quantitative models that describe newly observed phenomena increasingly limits the
progress in the field. While the fundamental techniques of modeling such as density func-
tional theory, quantum and classical Monte Carlo (MC) methods, molecular dynamics,
and fast multigrid algorithms are well known, new insights come from the application of
these methods in the field of nanoscience. Advances in computer technology and increase
in computational capabilities have made possible the modeling and simulation of com-
plex systems with millions of degrees of freedom. However, the full potential of novel
1
2 Computational Nanotechnology: Modeling and Applications with MATLAB®

theoretical and modeling tools has not been reached yet. Realizing this potential, however,
will require a concerted effort in theoretical and modeling research to overcome some of
the computational challenges in the field. For example, although our ability to synthe-
size and fabricate various nano-building blocks (nanotubes, quantum dots, clusters, and
nanoparticles) with novel and useful properties is steadily improving, we lack the ability
to incorporate them into complex, functional systems, and we do not fully understand the
theoretical intricacies of such systems.
There are many theoretical and modeling challenges to overcome in nanoscale studies. Just
to mention a few of such challenges: (i) to bridge electronic through macroscopic length
scale and timescale, (ii) to determine the transport mechanisms at the nanoscale, (iii) to
devise theoretical and simulation approaches to study nano interfaces, (iv) to describe
with reasonable accuracy the response of nanoscale structures to external probes such as
electric/magnetic fields, and so on. With each fundamental theoretical and computational
challenge that must be met in nanoscience come opportunities for research and discov-
ery. New tools and techniques (e.g., scanning tunneling microscopes and atomic force
microscopes) are giving us the ability to put atoms and molecules where we want them.
Researchers are discovering new properties that emerge at nanometer length scales that
are different from the properties of both individual atoms/molecules and bulk materials.
Scientists and engineers have successfully synthesized and characterized a broad range
of nano-building blocks with novel and potentially useful properties. Thus, nanoscale
science and technology raise research issues that are fundamental to a growing number
of disciplines and also display the potential for applications of enormous economic and
social significance.
In recent years, interest in the area of nanotechnology has exploded nationwide with
many universities and groups of researchers working in different aspects of nanotech-
nology. This work has allowed scientists a share in the nanotechnology research and has
created strong educational and research programs focusing on nanotechnology and insti-
tute interdisciplinary partnerships across field and disciplinary boundaries. Because of
the variety and large number of nano-building blocks and structures, it is impossible to
cover all of them. Therefore, in this work we will try to give a brief overview of only two of
such nanoscale systems, namely, molecular magnets and semiconductor quantum dots. While
we will look more closely into the theory and modeling of these two nanoscale systems, we
will also briefly address some of the critical research issues in the fast-evolving field of
nanomagnetism and nanoelectronics where molecular magnets and quantum dots are
the respective building blocks. Clearly, a full understanding of the properties of these two
very important characteristics of nano-building blocks is imperative for the whole field of
nanoscience for a number of reasons. Just as knowledge of the atom allows us to make and
manipulate larger structures, knowledge and accurate modeling of such nano-building
blocks will allow us to reliably manufacture larger artificial structures with prescribed
properties. This is the centerpiece of new functional nanomechanical, nanoelectronic, and
nanomagnetic devices.
Molecular magnets and semiconductor quantum dots are well defined by experiment
and are tractable using standard theoretical and computational tools. Moreover, they have
been demonstrated to hold promise in future technologies. To this effect any complete
theoretical and modeling initiative aiming to understand such systems should focus on
(i) creating a unique theoretical and modeling expertise, (ii) exploring novel theories and
models to predict behavior and reliability of functional nano-size sensors and devices,
and (iii) understanding classical transport mechanisms at nanoscales. Last but not
least, all these efforts should contribute to educate and train the first generation of truly
Introduction to Computational Methods in Nanotechnology 3

multidisciplinary nanoscientists and engineers for positions of leadership in academia and

industry, as well, maximize the benefits to society by stimulating the creation of new tech-
nologies and developing innovative solutions. On these lines, there are great potentials
for nanotechnology applications in the field of biology and medical sciences since there is
a convergence in length scales between inorganic nanostructures and biomolecules such
as DNA and proteins. First steps are very promising, for example, nanostructures such as
quantum dots are already being used as biosensors.
For a long time, magnets have found a wide range of applications in science and technol-
ogy; however, molecular magnets belong to a field that is still at an early stage of develop-
ment. Research interest in this field is motivated by the need for a better understanding
of the fundamental principles that govern magnetic behavior, in particular, when moving
from isolated molecules to bulk solids, as well as the need for new improved magnetic
materials. The trend toward devices to the ultimate scale—the molecular one—is a force
driving the expansion of this field. Molecular chemistry has already shown the capability
to synthesize new magnetic systems in mild conditions (from solutions, at room tempera-
ture) with specific magnetic and electronic properties.
Among the many advances in the field of nanotechnology, invention of sophisticated
experimental tools has made possible the fabrication of various nanoscale semiconductor
structures in a precise and controlled way. In such semiconductor devices, electron’s quan-
tum mechanical nature dominates. The payoff of this behavior is that electronic devices
built on nanoscale not only can pack more densely on a chip but also can operate far faster
than conventional transistors. With the shrinking size of these devices, electrons manifest
pronounced quantum behavior and their motion becomes confined with confinement that
can happen in one, two, or three dimensions.
The great progress achieved on fabricating nanoscale molecular magnets and nanoscale
semiconductor quantum dot devices has opened up a new frontier, whose aim is the ulti-
mate miniaturization of such nanoscale systems. The current–voltage characteristics of
such atomic and molecular systems hold the promise of revolutionary new devices for
ultrasensitive probes and detectors, very high-speed and ultra-large density electronic
components, and new electrochemical energy storage devices and the possibilities of novel
logic layouts. Indeed, recent demonstrations of molecular-based logic gates and nonvola-
tile random access memory have already been realized and point to the exciting possibili-
ties of molecular devices, and perhaps even quantum computing.
However, from a theoretical point of view, the accurate prediction of the properties of
various nanodevices, such as the calculation of current–voltage characteristics from first
principles, remains a serious challenge. Clearly, given the increased scientific and tech-
nological interest in this field of research, there is a need for new computational meth-
ods to investigate the fundamental properties of nanoscale systems. New computational
methods definitely will impact further advances in physics, chemistry, and engineering.
A better quantitative understanding of the properties of such nanoscale systems at dif-
ferent conditions is critical to achieve a quick commercialization of potentially ground-
breaking novel nanoelectronic and nanomagnetic devices.
Studies of the above-mentioned two nano-building blocks, molecular magnets and
semiconductor quantum dots, offer great promise for the future but will require new theo-
retical approaches and computationally intensive studies. Current algorithms and numeri-
cal methods must be made more efficient and new ones should be invented. Currently,
molecular dynamics simulation methods can handle systems with tens of thousands of
atoms; however, to fully exploit their power, algorithms need to be made scalable and fully
parallelized. Computational methods are especially useful in providing benchmarks for
4 Computational Nanotechnology: Modeling and Applications with MATLAB®

nano-building blocks, where experimental data are unreliable or hard to reproduce. Lack
of clear prescriptions for obtaining reliable results in nano blocks is another challeng-
ing problem for experiment and theory. While new experiments will need to be designed
to ensure reproducibility and the validity of the measurements, the theoretical chal-
lenge is to construct new theories that would cross-check such conclusions. While great
strides have been made in various simulation methods, a number of fundamental issues
remain. In particular, the diversity of time and length scales remains a great challenge at
the nanoscale. Intrinsic quantum attributes like transport and charge transfer remain a
challenge to incorporate into classical description. For example, at best, quantum Monte
Carlo (QMC) simulation methods are effective and easy to implement only at zero or very
low temperatures. Even though the QMC method and its many variants are currently the
most accurate methods that can be extended to systems in the nanoscience range, major
improvements are needed.
To conclude, there is a compelling effort being made to bring a wide range of multi-
disciplinary scientists to work together to understand phenomena in nanoscience, uti-
lizing various modeling approaches and tools. One of such powerful tools that can be
used successfully to study the basic properties of various nanoscale systems is MATLAB®.
Modeling with MATLAB attempts to give a brief and basic understanding of a key and
versatile tool that can be used effectively in many computational settings.

1.2 Molecular Magnetism

Research into molecular magnetism and the closely related field of molecular electronics is
quite new but very active. The interest in the magnetic properties of synthesized molecular
clusters [3,4] containing relatively small numbers of paramagnetic ions has only increased
in the recent years. With the ability to control the placement of magnetic moments of diverse
species within stable molecular structures, one can test basic theories of magnetism and
explore the design of novel systems that offer the prospect of useful applications [5,6].
Recent successful efforts in synthesizing solid lattices of weakly coupled molecular clus-
ters containing few strongly interacting spins has opened up the possibility of experimen-
tally studying magnetism at the nanoscale. Due to the presence of organic ligands, which
wrap the molecular clusters, the intercluster magnetic interaction is vanishingly small
when compared to intracluster interactions; therefore, the properties of the bulk sample
reflect the properties of independent individual nanoscale molecular clusters. The mag-
netic ions in each molecular cluster can be generally arranged in different ways, giving
rise to structures of very high symmetry (e.g., rings) and/or of lower symmetry presenting
other important features.
A common feature of these organic-based molecular magnets is that intermolecu-
lar magnetic interactions are extremely weak compared to intramolecular interactions
(within individual molecules). As a result, a bulk sample can be described in terms of
independent individual molecular magnets. As examples of molecular magnets with
ultrasmall numbers of embedded paramagnetic ions, we mention two dimer systems,
one [7] consisting of V 4+ ions (spin 1/2) and the other [8] Fe3+ ions (spin 5/2): a non-
regular triangular array [9] of Fe3+ ions (spin 5/2), a nearly equilateral triangular array
[10] of V 4+ ions, a nearly square array [11] of Nd 3+ (spin 9/2), a regular tetrahedron array
[12] of Cr 3+ (spin 3/2), and a non-regular tetrahedron array [13] of Fe3+ (spin 5/2) ions.
Introduction to Computational Methods in Nanotechnology 5

Also noteworthy is the pyrochlore antiferromagnet Tb2Ti2O 7, although distinct from the
class of organic molecules yet sharing the feature that the Tb3+ ions (spin 6) reside on a
network of very weakly coupled tetrahedra [14].
Early work on molecular magnetic clusters [15] recognized only antiferromagnetic (AF)
coupling, but later it has been realized that ferromagnetic (F) coupling is also possible [16].
In many of these clusters, the individual molecules appear to make independent contri-
butions to the bulk magnetic susceptibility, that is, the intermolecular magnetic interac-
tions between different molecular clusters are negligible so that the magnetic properties
are solely determined by the intramolecular couplings of spins within a given molecular
cluster. A very common choice of paramagnetic ion is Fe3+, which has a large spin (spin
5/2) and for which classical spin formalism is directly applicable, except at sufficiently low
temperatures [17–19]. There are indications that even a classical Heisenberg spin model
provides a very satisfactory description of a ring of eight Cr 3+ ions (spin 3/2), again except
at very low temperatures. The complex known as Fe4 is well described [13] by such a clas-
sical spin model. For AF exchange it turns out that the magnetic frustration of this system
is a very intricate function of temperature, magnetic field, and the ratio of two coupling
constants. In particular, the well-known molecular magnets, Fe8 and Mn12, have attracted
considerable interest in recent years. The Fe8 cluster is formed of 8 Fe3+ ions (spin 5/2). The
ground state spin is large, S = 10 and the system has competing AF interactions. The eight
iron atoms are split in two sets: six with moments parallel to the applied field and two with
moments antiparallel to the applied field [20]. The Mn12 cluster is formed of 6 Mn2+ ions
(spin 5/2) and 4 Mn3+ ions (spin 2). The ground state spin is again large, S = 12 and compet-
ing AF interactions do occur. It is now well understood that magnetization happens only
at the Mn sites and not on the ligands. In both cases, the magnetic moment of each molecule
sees a barrier characterized by 2S + 1 energy levels and a magneto-crystalline anisotropy.
For some values of the applied field, the levels from one side of the barrier “see” the lev-
els from the other side, and the phenomena of quantum tunneling of the magnetization
occurs, leading to rapid jumps in the magnetic moment in the sample. Magnetic clusters,
such as Fe8 and Mn12, with high spins in the ground state and Ising-type anisotropy show
slow relaxation of the magnetization at low temperature, which eventually relaxes with a
tunneling mechanism.
Because of the relatively large value of spin it turns out that many molecular magnets
can be described to very high accuracy [21] at sufficiently high temperatures, by using the
classical Heisenberg spin model, with exchange interaction between classical unit vectors.
Only for sufficiently low temperatures, one needs to incorporate the quantum character of
the spins. This underscores the potential utility of a classical spin treatment in its ability
to provide useful results. It is perhaps surprising that even this route is fraught with dif-
ficulties. One might expect that the determination of the partition function for a few-spin
system would be a relatively simple task. However, to put this matter in perspective, it
should be recalled that for a finite open chain of classical spins, which interact with nearest-
neighbor isotropic Heisenberg exchange, the partition function has been evaluated only
in the absence of an external magnetic field [22]. For the related system, where the linear
chain is closed so as to form a Heisenberg ring, the calculation of the partition function and
related magnetic properties is extremely involved. Exact, unwieldy infinite series expan-
sions of these quantities were successfully derived by Joyce [23] many years ago, but only
for zero magnetic fields. For more complicated models where we have at least two differ-
ent exchange interactions, no solutions can be obtained following Joyce’s method. With the
introduction of an external magnetic field the analytic calculation of the partition function
has been an intractable problem even for small numbers of interacting spin moments [24,25].
6 Computational Nanotechnology: Modeling and Applications with MATLAB®

From the theoretical point of view, there is a great interest to study the exact nature of
the ground state of molecular magnets and explain the observed properties given that one
of the great attractions of the whole field is the potential to build compounds that behave
as classical solid state magnets. This way we would be able to fabricate structures that
exhibit completely new properties, such as wide range of magnetic ordering temperatures,
so that the relationship between magnetism and temperature can be precisely controlled.
The other principal focus is to provide the theoretical underpinnings for designing such
structures. The challenging theoretical goal is to obtain a deeper understanding of how
electronic and molecular structures (spin density, band structure and anisotropy) relate to
macroscopic physical properties (magnetic and electrical). Thus, there is a great need for a
much stronger fundamental science base to underpin the developments of novel magnetic
materials for useful applications in the future.
To reach this point, several fundamental problems are still to be solved, such as under-
standing the details of molecular forces, the nature of interactions between molecules,
the properties of the molecule itself, and the way to bridge systems from a single-
molecule level to the macroscopic world. Of concern is also the interaction between spin
carriers. Several properties are relevant here: overlap and orthogonality, spin delocal-
ization, spin polarization effects, which are probably relevant in cases involving mobile
electrons, etc.
Obviously, the initial task from the perspective of theory and modeling of nanoscale
molecular magnetic systems is to construct a spin Hamiltonian from a given set of experi-
mental data. For the sake of simplicity, in this review, we assume that the spin Hamiltonian
can be quite arbitrarily written in the form
   
H= ∑ J ijSi ⋅ Sj − μ ∑ B ⋅ Si , (1.1)

where
S⃗ i and S⃗ j are the respective magnetic spins at site i and j
Jij is the coupling term between a pair of spins
B⃗ is the applied magnetic field
μ is the gyromagnetic factor

and in a short hand notation the first term incorporates all types of spin–spin interac-
tions (exchange and magneto-crystalline anisotropy). The relative order of magnitude of
various spin Hamiltonian terms should be in agreement with the experimental results.
Generally, such type of information can be fairly easily extracted for all previously men-
tioned cases of molecular magnets.
If we claim that we know the Hamiltonian, then the difficult task to carry out is the
analytical/computational calculation of the properties of the system using any desirable
level of theoretical and/or numerical sophistication: from semiempirical treatments to
ab initio all particle computations. Since analyzing even relatively small assemblies of
molecules in real time and space involves a large amount of computing power, MC meth-
ods, in which the overall properties of a molecular cluster are analyzed by considering
just a sample of them, can be used successfully. Despite known shortcomings, modeling
efforts of this nature have been successful to shed light and achieve a better under-
standing of key phenomena in the field of nanoscale magnetism: (i) tuning of the Curie
temperatures and/or coercive fields, (ii) understanding bistable systems, where the elec-
tronic spin can change direction under influence of external factors such as pressure or
Introduction to Computational Methods in Nanotechnology 7

thermal energy with obvious potential for future molecular electronic switching or
display devices, (iii) understanding how magnetism is modified by conducting and super-
conducting materials and bistable materials where magnetic properties change abruptly,
and (iv) understanding the transitional range between quantum and classical systems,
just to mention a few.
Since our objective is not to give a broad overview of the subject of nanoscale molecular
magnetism, in the following, we focus our attention on low nuclearity complexes consist-
ing of clusters of few spins. These structures, while easier to handle, are also ideal pro-
totypes to illustrate the application of various computational and modeling tools. At the
same time few-spin molecular magnets are likely to represent the “molecular” nanoscale
building bricks for the formation of high-nuclearity larger molecular clusters. Therefore,
their characterization is an essential step for broader studies targeting larger magnetic
systems.
The spin dynamics of these nanoscale magnetic clusters is of particular interest since
it can directly be probed by different experimental methods such as nuclear magnetic
resonance (NMR) [26]. In view of the importance of knowing the dynamical behavior
of spin–spin correlation functions, it is most desirable to find model systems, which can
be solved exactly. This way one can test the regimes of validity of various experimen-
tal results and theoretical approximation schemes. Among the variety of spin–spin cor-
relation functions, the time-dependent spin autocorrelation function is closely linked
with spin dynamics; therefore, it is natural to focus on this quantity. Earlier studies have
numerically investigated the time-dependent spin autocorrelation function of many-spin
systems, for instance, a classical Heisenberg model with nearest-neighbor exchange inter-
action between spins [27,28]. The goal of these simulations was the study of the expected
power-law decay of the long-time spin autocorrelation function for many-spin systems at
infinite temperature [29].
In this work, we focus on the spin dynamics of ultrasmall, nanoscale molecular magnets
consisting of coupled classical (high) Heisenberg spins. In particular, we give exact expres-
sions (in integral form) for the time-dependent spin autocorrelation function at arbitrary
temperatures for a dimer system of classical (high) spins that interact with both exchange
and biquadratic exchange interactions. The mathematical difficulty to solve exactly the
equations of motion and to perform the phase-space average for interacting spins makes
an exact analytical calculation of the time-dependent spin autocorrelation function very
challenging, even for the ultrasmall system considered here. To overcome these mathemat-
ical difficulties, we introduce a method, which simplifies the calculation of various quanti-
ties through the introduction of suitably chosen auxiliary time-independent variables into
an extended phase-space integration. The present analytic results, although derived for
the dimer system of spins [30], can provide useful benchmarks for assessing numerical
methods that calculate the time-dependent spin dynamics of other more complex high-
spin magnetic systems.
The Hamiltonian of a dimer system of spins with exchange and biquadratic interaction
is written as follows:
    2
H (t) = JS1(t)S2 (t) + K ⎡S1(t)S2 (t)⎤ , (1.2)
⎣ ⎦

where
J and K represent, respectively, the exchange and biquadratic exchange interactions
S⃗ i (t) are time-dependent classical spin vectors of unit length (i = 1, 2)
8 Computational Nanotechnology: Modeling and Applications with MATLAB®

The orientation of the classical unit vectors, S⃗ i (t), at a moment of time, t, is specified by
polar and azimuthal angles, θi(t) and φi(t), which, respectively, extend from 0 to π and
0 to 2π. The exchange interaction between a pair of spins can be either AF, J = |J| > 0, or
F, J = −|J| < 0. The biquadratic exchange interaction, K, can be positive, zero, or negative.
At an arbitrary temperature, T, the time-dependent spin autocorrelation function, CT (t) =
〈S⃗ i (0)S⃗ i (t)〉, is evaluated as a phase space average over all possible initial time orientations
of the spins:
   

CT (t) =
∫ ∫
dS1(0) dS2 (0)exp [ −βH (0)] Si (0)Si (t)
, (1.3)
Z(T )

where
i = 1 or 2 is a selected spin index
dS⃗ i (0) = dθi(0)sin[θi(0)]dφi(0) is the initial time solid angle element appropriate for the ith
spin, β = 1/(kBT)
kB is Boltzmann’s constant

The denominator of Equation 1.3 represents the partition function

 
∫ ∫
Z(T ) = dS1(0) dS2 (0)exp [ −βH (0)] , (1.4)

where H(0) is the initial time Hamiltonian of the spin system. In order to evaluate the time-
dependent spin autocorrelation function, we need first to solve the equations of motions
for the spins and then perform the angular average over all possible initial time spin ori-
entations in the phase space.
The dynamics (equations of motion) of classical spins is determined from

d   ∂H (t)
Si (t) = −Si (t) ×  , (1.5)
dt ∂Si (t)

where the set of solutions, {S⃗ i (t)}, depends on the initial orientation of the spins, {S⃗ i (0)}.
The calculation of CT(t) follows several steps: (i) solve the equations of motion for the spins
to obtain S⃗ i (t), (ii) calculate the partition function Z(T), and (iii) compute the integrals appear-
ing in the numerator of Equation 1.3. By applying Equation 1.5 to each spin of the
dimer, it is not difficult to note that the total spin, S⃗ (t) = S⃗ 1(t) + S⃗ 2(t), is a constant of motion,
S⃗ (t) = S⃗ (0) = S⃗ , and as a result we can rewrite Equation 1.5 as

d   
Si (t) = − ⎡⎣ J + K (S2 − 2)⎤⎦ Si (t) × S , (1.6)
dt

where S⃗ represents the constant total spin.

The above differential equations for spins can be exactly solved in a new coordinate system
(x′y′z′) in which the constant vector S⃗ lies parallel to the z′ axis. Let us denote (αi, βi) to be the
polar and azimuthal angles of spin S⃗ i (0) with respect to the new coordinate system in which
the direction of S⃗ defines the z′ (polar) axis. It follows that S cos (α i) = S⃗ i (0)S⃗ . The solution
Introduction to Computational Methods in Nanotechnology 9

of Equation 1.6 for each spin component of S⃗ i (t) depends on the sign of [J + K(S2 − 2)].
Irrespective of the sign of [J + K(S2 − 2)], we find that the quantity S⃗ i (0)S⃗ i (t) is given by the
expression
 
Si (0)Si (t) = sin 2 (α i )cos [ ω(S)t ] + cos 2 (α i ), (1.7)

where ω(S) = |J + K(S2 − 2)|S denotes a precession frequency and 0 ≤ S = |S⃗ | ≤ 2. Note that
S⃗ i (0)S⃗ i (t) does not depend on the ith spin azimuthal angle βi.
In as much as the spins are equivalent, without loss of generality, we fix i = 1 and concen-
trate on the calculation of CT (t) = 〈S⃗ 1(0)S⃗ 1(t)〉. From the definition of the total spin variable, S⃗ =
S⃗ 1(0) + S⃗ 2(0), recalling that S cos(α1) = S⃗ 1(0)S⃗ , we easily find that 1 + S⃗ 1(0)S⃗ 2(0) = S cos(α1). Since
the product S⃗ 1(0)S⃗ 2(0) is expressible in terms of the total spin as S⃗ 1(0)S⃗ 2(0) = S2/2 − 1, it follows
that cos(α 1) = S/2 and depends only on the total spin magnitude. Through these simple
mathematical transformations, we obtain
  ⎛ S2 ⎞ S2
F(t , S) = S1(0)S1(t) = ⎜ 1 − ⎟ cos [ ω(S)t ] + . (1.8)
⎝ 4⎠ 4

Using a similar procedure, the Hamiltonian can be written in terms of the total spin
variable as
J 2 K
H(t) = H(0) = (S − 2) + (S 2 − 2)2 , (1.9)
2 4

and is a constant of motion.

By expressing all relevant quantities in terms of the total spin variable, which is a con-
stant of motion, we now apply our calculation method whose success is based on the
observation that the values of all multidimensional integrals, for example Z(T), are left
unchanged if multiplied by unity, which is written as follows:

d3q    
∫ ∫
d 3S
(2π) 3 ⎢
⎣ ( )
exp ⎡iq S − S1(0) − S2 (0) ⎤ = 1.
⎥⎦
(1.10)

Note that the above identity originates from the well-known formula,
  
d 3Sδ ( 3 )
∫
⎡S − S1(0) − S2 (0)⎤ = 1, that applies to a three-dimensional (3D) Dirac delta function.
⎣ ⎦
Subsequent calculations are straightforward given that both H(0) and S⃗ 1(0)S⃗ 1(t) appearing
in Equation 1.3 can be expressed solely in terms of S. As a result, the integrations over
individual spin variables pose no problems. For the partition function, we obtain
2
⎡ βJ βK 2 ⎤
0
∫
Z(T ) = ( 4π)2 dSD(S)exp ⎢ − (S 2 − 2) −
⎣ 2 4
(S − 2)2 ⎥ ,
⎦
(1.11)

d3 q 
where D(S) = 4πS2
∫ ( 2π )3 exp(iqS )(sin q/q)2 can be calculated analytically and is

⎧S/2 0<S<2
⎪
D(S) = ⎨S/4 S=2 (1.12)
⎪0 S > 2.
⎩
10 Computational Nanotechnology: Modeling and Applications with MATLAB®

The vanishing of D(S) for S > 2 reflects the constraint that the total spin cannot exceed 2.
Note that for K = 0, the partition function becomes Z(T ) = ( 4π)2 sinh(βJ )/βJ . For J ≠ 0 and
K ≠ 0, the integral in Equation 1.11 can be expressed analytically in terms of error functions.
From the perspective of numerical calculations, the one-dimensional (1D) integral form in
Equation 1.11 is better suited. The integral appearing in the numerator of Equation 1.3 is gen-
erally very difficult to calculate. However, using the method illustrated above, one obtains
2
( 4 π )2 ⎡ βJ βK 2 ⎤
CT (t) =
Z(T ) ∫ dS D(S)exp ⎢⎣− 2 (S
0
2
− 2) −
4
(S − 2)2 ⎥ F(t , S).
⎦
(1.13)

The integrals appearing in Equation 1.13 can be carried out analytically using MATLAB.
The final result can be written in a closed form in terms of error functions. The expressions
are quite lengthy and cumbersome. Because of such undesired complexity, the 1D inte-
gral representation in Equation 1.13 not only suffices but also is preferable for all practical
needs. The preceding formula for CT(t) represents the exact expression (in integral form) for
the time-dependent spin autocorrelation function of such a system. We now study in detail the
time dependence of CT(t) for the extreme case of very low temperature (we choose a typical
value, kBT/|J| = 0.1). In Figures 1.1 and 1.2, we consider an AF exchange interaction, J =
|J| > 0, and, respectively, nonnegative K = |K| ≥ 0 and non-positive K = −|K| ≤ 0. The AF
case of J = |J| > 0 and K = |K| ≥ 0 shown in Figure 1.1 is rather interesting. One notes that
CT (t) dramatically changes its time dependence from a smooth function to a strongly oscil-
latory function of |J|t when |K|/|J| increases and becomes larger or on the order of unity.
For vanishing biquadratic exchange interaction (K = 0), the infinite-time limit of the spin
autocorrelation function is
1
CT (t → ∞) = ⎡1 − L(βJ )⎤⎦ ; K = 0, (1.14)
2⎣

1.2
J > 0 K = 0 |K |/|J| = 0.0
1 J > 0 K > 0 |K |/|J| = 0.3
J > 0 K > 0 |K |/|J| = 1.0
0.8

0.6
CT (t)

0.4

0.2

–0.2

–0.4
0 10 20 30 40 50 60
|J| t

FIGURE 1.1
Time-dependent spin autocorrelation function, CT(t), for the classical dimer of spins with exchange and biqua-
dratic exchange interactions at a very low temperature, kBT/|J| = 0.1. Given an AF exchange interaction between
spins, J = |J| > 0, we consider several nonnegative values of the biquadratic exchange interaction, K = |K| ≥ 0.
Note how CT(t) changes from a very smooth function of |J| t for small values of |K|/|J|, to a strongly oscillatory
function of |J| t as |K|/|J| becomes comparable or larger than one.
Introduction to Computational Methods in Nanotechnology 11

1.2
J > 0 K = 0 |K|/|J| = 0.0
1 J > 0 K < 0 |K|/|J| = 0.5
J > 0 K < 0 |K|/|J| = 1.5
0.8

0.6
CT (t)

0.4

0.2

–0.2

–0.4
0 10 20 30 40 50 60
|J| t

FIGURE 1.2
Time-dependent spin autocorrelation function, CT(t), for the classical dimer of spins with exchange and biqua-
dratic exchange interactions at a very low temperature, kBT/|J| = 0.1. Given an AF exchange interaction between
spins, J = |J| > 0, we consider several non-positive values of the biquadratic exchange interaction, K = −|K| ≤ 0.
Note that there are no relevant qualitative changes on the dependence of CT(t) as a function of |J| t as |K|/|J|
varies. Qualitatively speaking, CT(t) remains a smooth function of |J| t with a minimum that deepens and
occurs sooner as |K|/|J| increases.

1.1
J < 0 K = 0 |K|/|J| = 0.0
1.05 J < 0 K > 0 |K|/|J| = 0.1
J < 0 K > 0 |K|/|J| = 0.3

1
CT (t)

0.95

0.9

0.85

0.8
0 10 20 30 40 50 60
|J| t

FIGURE 1.3
Time-dependent spin autocorrelation function, CT(t), for the classical dimer of spins with exchange and biqua-
dratic exchange interactions at a very low temperature, kBT/|J| = 0.1. Several nonnegative values of the biquadratic
exchange interaction, K = |K| ≥ 0, are considered for a given F exchange interaction, J = −|J| < 0. When |K|/|J|
increases from 0.0 to 0.1, the oscillations of CT(t) amplify, but for larger values of |K|/|J| the function gradually
transforms into a smooth function of |J| t with fast decaying oscillations.

where L(z) = coth(z) − 1/z is Langeven’s function. In Figures 1.3 and 1.4 we consider an F
exchange interaction, J = −|J| < 0, and, respectively, nonnegative K = |K| ≥ 0 and non-
positive K = −|K| ≤ 0.
Contrary to what is seen in Figure 1.1, the case described in Figure 1.3 for J = −|J| < 0
and K = |K| ≥ 0 shows a very different behavior, in the sense that the strong oscillatory
12 Computational Nanotechnology: Modeling and Applications with MATLAB®

1.1
J < 0 K = 0 |K|/|J| = 0.0
1.05 J < 0 K < 0 |K|/|J| = 0.1
J < 0 K < 0 |K|/|J| = 0.3

CT (t) 1

0.95

0.9

0.85

0.8
0 10 20 30 40 50 60
|J| t

FIGURE 1.4
Time-dependent spin autocorrelation function, CT(t), for the classical dimer of spins with exchange and biqua-
dratic exchange interactions at a very low temperature, kBT/|J| = 0.1. Several non-positive values of the
biquadratic exchange interaction, K = −|K| ≤ 0, are considered for a given F exchange interaction, J = −|J| < 0.
Note that CT(t) approaches its long-time asymptotic limit value (that is larger for larger values of |K|/|J|) with
less pronounced oscillations as |K|/|J| increases.

dependence of CT (t) as a function of |J| t is suppressed when |K|/|J| increases. One clearly
notes that for low temperatures the spin autocorrelation function is dominated by the low-
est frequency (S ≈ 0) when we have AF coupling and by the highest frequency (S ≈ 2) for
the F case.
To conclude, we modeled and studied the spin dynamics and time-dependent spin
autocorrelation function for a nanoscale molecular magnet consisting of a dimer system
of Heisenberg spins interacting with exchange and biquadratic exchange interactions.
By using a method that introduces the total spin variable into the defining expression of
the time-dependent spin autocorrelation function, we obtain the exact analytic expres-
sion (in integral form) for this quantity at an arbitrary temperature. Using MATLAB it
was straightforward to model and compute either numerically or analytically the various
quantities of interest for such a nanoscale spin structure.

1.3 Semiconductor Quantum Dots

Semiconductor quantum dots are fabricated nanostructures in which charge carriers, such
as few electrons, are confined in a small spatial region in a host crystal. In typical semi-
conductor heterostructures, such as GaAs/AlGaAs, the number of electrons confined in a
quantum dot can be changed by adjusting the external electric potential of the metallic
electrodes (gates). The size and shape of these nanostructures, and, therefore, the num-
ber of electrons they contain can be precisely controlled. In many cases, the confinement
potential of the electrons in the quantum dot region is quasi-parabolic and the number of
trapped electrons varies from few to thousands of electrons.
Quantum confinement profoundly affects the behavior of the system’s electrons [31],
greatly influencing their interactions with each other and with external parameters, such
Introduction to Computational Methods in Nanotechnology 13

as a magnetic field. Quantum confinement of electrons is just one of several ways quantum
mechanics reveals itself. Another pure quantum phenomena associated with electrons is
their spin. Generally, the Bohr radius (size) of quantum dots is much larger than the Bohr
radius of real atoms. This implies that ordinary magnetic fields (on the order of 1 T) control
magneto-transport properties of quantum dots. An external magnetic field affects both
orbital and spin motion of electrons. External control of the full quantum wave function in
a semiconductor quantum dot may lead to novel technological application involving both
charge and spin. Thus, there is great interest on the properties of electronic materials, such
as single and coupled two-dimensional (2D) semiconductor quantum dots in presence of a
magnetic field. From the theoretical point of view, a magnetic field applied perpendicular
to the 2D dot plane will change the nature of single electron levels from those of the har-
monic oscillator to Landau levels. The electronic spectrum will consist of discrete energy
levels but will strongly depend on the applied perpendicular magnetic field, which also
affects the electron’s spin.
The importance of semiconductor quantum dots lies primarily in their tunability and
sensitivity to external parameters as electrons are confined in all dimensions. As a result
semiconductor quantum dots represent a unique opportunity to study fundamental quan-
tum theories in a tunable atomic-like set-up. From a practical point of view, semiconduc-
tor quantum dots have great potentials to realize novel nanoelectronic devices and new
research directions on these lines are emerging every time.
In this work, we want to give a brief review of some of the theoretical and modeling
approaches used in studies of semiconductor quantum dots. We will specifically consider
only 2D few-electron semiconductor quantum dots. The main emphasis will be to clarify
the relations between different theories and numerical methods used to study the proper-
ties of few-electron 2D semiconductor quantum dots in an external tunable parameter, for
example, a magnetic field. While the focus will be on isolated 2D semiconductor quantum
dots containing few electrons, we point out that all adopted computational methods can
be straightforwardly implemented to studies of small arrays of coupled quantum dots in
which electrons in different quantum dots are weakly coupled to each other, for instance,
as in a double quantum dot [32,33].
In arrays of coupled quantum dots, for instance two laterally coupled quantum dots
[34,35], the inter-dot distance between nearest-neighbor quantum dots can be experimen-
tally adjusted. A given energy barrier separates the electrons of one dot from tunneling to
the other dot. A two-well potential (with finite range) can be used to model the coupling of
any two harmonic wells centered at a given distance apart. It is important to remark that
the study of weakly coupled arrays of semiconductor quantum dots is a subject of great
fundamental and practical interest since the magneto-transport properties of arrays of
quantum dots can be dramatically different from the properties of the individual quantum
dots that constitute them. While each individual quantum dot in the system still retains
the set of well-defined charge states like in an atom, tunneling of electrons between two
quantum dots may fundamentally change the individual properties of each of the quan-
tum dots including charging effects or Coulomb oscillations. In such coupled systems,
we may expect the electrons to reach a state similar to the “resonant tunneling condition”
state and thus freely transmit between the two quantum dots. A properly tuned external
field may then dramatically affect the behavior of the system, and novel magneto-transport
features are expected to arise in weakly coupled arrays of quantum dots. Under these
circumstances, the interplay between quantum confinement, electronic correlation, inter-dot
coupling, and magnetic field will be more subtle, and we expect to see many interest-
ing physical phenomena with possible technological applications. Quantum chemistry
14 Computational Nanotechnology: Modeling and Applications with MATLAB®

methods of molecular physics, which rely on knowledge of individual quantum dots, can
be used. While the study of arrays of coupled quantum dots is a difficult problem, the anal-
ogy between real atoms and quantum dots (“artificial atoms”) provides us with a power-
ful set of methods from molecular physics such as the valence bond Heitler–London (HL)
approach or the linear combination of atomic orbitals (LCAO) approach.
Since knowledge of a single isolated quantum dot is a key ingredient of all other more
elaborate treatments, we will focus our attention only on isolated 2D semiconductor quan-
tum dots containing a few confined electrons. Such nanoscale systems are a topic of inten-
sive ongoing research since they represent a whole new class of semiconductor devices
with promising properties to meet the new technological challenges of the twenty-first
century [36–40]. 2D semiconductor quantum dots are expected to provide the basis for
future generations of device technologies such as threshold-less lasers and ultradense
memories. Generally speaking, 2D quantum dots can be viewed as artificial atoms. They
hold only a few electrons in contrast to standard semiconductor devices; therefore, they
represent the ultimate limit of the semiconductor device scaling. As the device sizes are
reduced, the number of carriers involved in the operation of a single device is reduced as
well. In fact, state-of-the-art semiconductor structures will soon be plagued by dopant
fluctuation and particle noise problems. Quantum dot device concepts utilize the discrete-
ness of the electron charge and they offer a possible breakthrough in device and circuit
technology representing the ultimate limit of the semiconductor device scaling.
The physics of 2D semiconductor dots [41–47] shows many parallels with the behavior
of naturally occurring quantum systems in atomic and nuclear physics. The difference
is that in 2D quantum dots the confinement of electrons is due to an artificially created
potential formed by the electrodes connected to layers of semiconductor, while in atomic
systems, electrons are confined by the Coulomb attraction of the nucleus. As in an atom,
the energy levels in a 2D semiconductor quantum dot become quantized due to the con-
finement of electrons. Unlike atoms, however, 2D semiconductor quantum dots can be eas-
ily connected to electrodes and are therefore excellent tools to study atomic-like properties
in a controllable way. There is a wealth of interesting phenomena that have been seen
in 2D quantum dot structures over the past decade. Initial studies of 2D quantum dots
focused on their atomic-like properties [48–50] at low magnetic fields. In particular, the
capacitance spectroscopy of 2D quantum dots in the low-magnetic-field regime shows that
the ground states of parabolic 2D quantum dots exhibit shell structure and are believed
to obey Hund’s first rule [48]. The shell structure is particularly evident in measurements
of the change in electrochemical potential due to the addition of one extra electron. In this
regime, parabolic 2D quantum dots exhibit shell structure manifesting their atomic-like
nature. However, with the strengthening of the magnetic field, the structure of single-
electron levels changes to highly degenerate Landau levels and the electron correlations
play a very important role, similar to the fractional quantum Hall effect (FQHE) case seen
in bulk 2D electronic systems (2DES) [51–53]. Transport properties of 2D quantum dots in
this regime are highly interesting because of possible applications of the single-electron
tunneling in electronic devices [54] as well as use of such structures for quantum computa-
tion [55,56].
A standard theoretical model for 2D semiconductor quantum dots involves a number of
approximations. The most common approximations are (i) to consider the motion of elec-
trons exactly 2D, (ii) to consider a simplified confining potential (generally parabolic), and
(iii) to consider the interaction potential between electrons of bare Coulomb form. A mag-
netic field perpendicular to the plane of the 2D quantum dot acts as an external tuning
parameter for the confined system of electrons. The main effect of such a magnetic field, as
Introduction to Computational Methods in Nanotechnology 15

it becomes stronger, is to change the nature of single-electron levels from those for the 2D
harmonic oscillator to Landau levels. If the magnetic field is very strong, the energy levels
with different angular momentum become degenerate or quasi-degenerate. In this regime,
the electron correlations play a very important role, similar to what is seen in the FQHE in
bulk 2D electron systems in high magnetic fields [57,58].
The properties of N-electron 2D quantum dots subject to a magnetic field, B⃗ = (0, 0, Bz),
perpendicular to the dot plane are generally calculated by considering the following
Hamiltonian:
N
⎧ 1 ⎡ ˆ   2 N
e2
ˆ = ⎤ + V (ri )⎫⎬ + 1
H ∑
i =1
⎨
⎩ 2 m ⎢
⎣
pi + eA( ri )
⎦⎥ ⎭ 4πε 0 ε r
∑
i> j
  + gμ BBzSz ,
ri − rj
(1.15)

where
the first term is one-electron term
the second term is the Coulomb potential energy
the last term is the Zeeman energy
V(r⃗ ) is the one-electron confinement potential

The vector potential in a symmetric gauge is written as follows:

  B
A(r ) = z (− y , x , 0), (1.16)
2

where
r⃗ = (x, y) is the 2D position vector
−e (e > 0) is electron’s charge
m is electron’s mass
g is electron’s g-factor
μB is Bohr’s magneton
εr is the dielectric constant
Sz is the z-component of the total spin

To obtain the many-electron energy spectrum and wavefunctions one must solve the sta-
tionary Schrödinger equation for the Hamiltonian given earlier:
ˆ Ψ(r1 , … , rN ) = EΨ(r1 , … , rN ).
H (1.17)

Clearly, this is a formidable task and this quantum problem cannot be solved exactly even
for systems of as few as N = 2 electrons. The case of few-electron quantum dots [59–61] is of
particular interest, since single-electron confinement energy, the cyclotron energy for ordi-
nary magnetic fields, and electron–electron correlation are all on the same order of mag-
nitude. As a result, a rich physics and a variety of complicated phenomena are manifested.
For simplicity, we assume an isotropic parabolic confinement potential for the electrons,
m 2 2
V (r ) = ω0r , (1.18)
2

where
ħω0 is the parabolic confinement energy
r 2 = x2 + y2
16 Computational Nanotechnology: Modeling and Applications with MATLAB®

One can write the parabolic confinement potential in dimensionless units for energy
(potential) and length (distance) as follows:

V (r ) 1
= (αr )2 , (1.19)
ω 0 2

where

mω 0
α= , (1.20)


is the inverse quantum oscillator length. A plot of the dimensionless potential, V(r)/ħω0,
as a function of the dimensionless distance, αr, is given in Figure 1.5. The assumption of
parabolic confinement is a common choice for the electron’s confinement in a 2D semicon-
ductor quantum dot [62–65]. The parabolic confinement model explains reasonably well
some of the main features associated with most common quantum dots. That said, it is
important to remark that many other more realistic confinement potentials have also been
considered such as anisotropic potentials [66–68] and/or non-parabolic ones [69–71].
If we neglect the Coulomb interaction between electrons, the Hamiltonian in Equation
1.15 (without the Zeeman term) is reduced to a sum of single particle Hamiltonians, H0(r⃗ )
written as follows:

ˆ 0 (r ) = 1 ⎡ pˆ + eA(r )⎤ + m ω 02r 2 ,
2
H (1.21)
2m ⎣⎢ ⎦⎥ 2

where ħω0 is the strength of the parabolic confinement potential. The quantum problem
for such a Hamiltonian can be solved exactly and the eigenstates are routinely called the
Fock–Darwin (FD) states since Fock [72] and Darwin [73] were the first to investigate this
problem. The FD states are written as follows:

mz
⎛ r2 ⎞ ⎛ r ⎞ ⎛ r 2 ⎞ exp( −imzϕ)
Ψnmz (r , ϕ) = N nmz exp ⎜ − 2 ⎟ ⎜ Lnmz ⎜ 2 ⎟ × , (1.22)
⎝ 4lΩ ⎠ ⎝ 2lΩ ⎟⎠ ⎝ 2lΩ ⎠ 2π

10

8
Dimensionless V ( r)/ћω0

FIGURE 1.5
Dimensionless 2D parabolic confining 0
potential, V(r)/ħω0 as a function of the –6 –4 –2 0 2 4 6
dimensionless distance, αr. Dimensionless length αr
Introduction to Computational Methods in Nanotechnology 17

where
lΩ =  is an effective magnetic length
2mΩ
n = 0, 1, … is the radial quantum number
mz = 0, ±1, … is the z-angular momentum quantum number
m
Ln z ( z) are associated Laguerre’s polynomials [74]

The normalization constant is, N nmz = n! . The frequency Ω appearing in the

lΩ2 (n +|mz|)!
expression for the effective magnetic length is defined as follows:

ω c2
Ω 2 = ω 02 + , (1.23)
4

where ωc = eBz/m is the well-known cyclotron frequency. The discrete allowed energies
(without the Zeeman energy) are written as follows:

ω c
Enmz = Ω ( 2n + 1 + mz ) − mz , (1.24)
2

and depend on the magnetic field by means of the dependence of ωc on the magnetic
field. The energy spectrum of few FD states in dimensionless units is plotted in Figure 1.6,
which shows the dependence of ε = Enmz /(ω 0 ) as a function of the dimensionless magnetic
field parameter, ωc/ω0. The energy expression in Equation 1.24 predicts that energy levels
with positive mz shift downward and levels with negative mz shift upward as magnetic
field increases. Thus, electrons may undergo transitions in their quantum numbers as a
function of the magnetic field. When ω0 = 0 or in the limit of very large magnetic fields
(ωc >> ω0), the effective magnetic length, lΩ becomes the electronic magnetic length:

  ωc
lΩ → = ; → ∞. (1.25)
mω c eBz ω0

10

6
Energy (ε)

FIGURE 1.6
0 Single-particle energy levels, ε = Enmz /
0.5 1 1.5 2 2.5 3 3.5 4 (ω 0 ), as a function of the magnetic field
ωc/ω0 parameter, ωc/ω0.
Exploring the Variety of Random
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The Project Gutenberg eBook of The Last Lady of
Mulberry: A Story of Italian New York
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Title: The Last Lady of Mulberry: A Story of Italian New York

Author: Henry Wilton Thomas

Illustrator: Emil Pollak

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1900

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*** START OF THE PROJECT GUTENBERG EBOOK THE LAST

LADY OF MULBERRY: A STORY OF ITALIAN NEW YORK ***
The Last Lady of Mulberry
Flowers for a Neapolitan of the Porto!
(See page 53.)
The Last Lady
of Mulberry
A Story of Italian New York
By Henry Wilton Thomas

Illustrated by Emil Pollak

New York
D. Appleton and Company
1900
 Copyright, 1900
By HENRY WILTON THOMAS

All rights reserved

 CONTENTS
CHAPTER PAGE
I. —A goddess scorned 1
II. —Casa Di Bello 18
III. —A spot of yellow paint 37
IV. —Juno the Superb 44
V. —The First Lady 57
VI. —Carolina resolves to go courting 75
VII. —A flutter in the Tomato Bank 82
VIII. —Juno performs a miracle 94
IX. —The Perpetua meets a bear 102
X. —Birth of the Last Lady 114
XI. —A race to the swift 123
XII. —The peace preserved 143
XIII. —The peace disturbed 153
XIV. —Yellow boots and orange blossoms 172
XV. —Failure of Banca Tomato 186
XVI. —The Last Lady unmasked 211
XVII. —The falcon saves the dove 228
XVIII. —At the altar of San Patrizio 238
XIX. —Events wait upon the dandelions 255
XX. —A house divided 268
XXI. —The feast of springtide 278
XXII. —Carolina constructs a drama 292
XXIII. —A partnership in ten-inch St. Peters 308
XXIV. —Two troublesome wedding gifts 314
 LIST OF ILLUSTRATIONS
FACING PAGE
Flowers for a Neapolitan of the Porto! Frontispiece
Would Genoa be the same when his Juno and
Peacock
should be there? 5
Bertino’s arrival at Paradise Park 20
The bear-tamer’s wife 109
“A broken leg! Dio Santo!” 111
It was a wild thrust 170
Bridget in balia array 189
Jack Tar’s ignoble end 196
The Last Lady as Queen of the Feast 287
THE LAST LADY OF MULBERRY
 CHAPTER I
A GODDESS SCORNED

All Armando knew of sculpture he had learned from his uncle

Daniello, a mountain craftsman who never chiselled anything greater
than a ten-inch Saint Peter. At night in the tavern on the craggy
height, with a flask of barbera before him, the old carver would talk
grandly of his doings in art, while his comrades, patient of the oft-told
tale, nodded their heads in listless but loyal accord. They all knew
very well that it was young Armando who did most of the carving, yet
they cried “Bravo!” for old Daniello’s wine was good. And so it had
been for a long time. While the lad chipped all day in a little
workshop perched beyond the nether cloud shadows, his uncle
passed the hours in Genoa, where, by sharp wits and bland tongue,
he transmuted the marble into silver.
But Armando had a soul that looked far above the gleaming
tonsures of ten-inch Saint Peters. Wherefore he was unhappy. When
his twentieth birthday dawned it seemed to him that his life had been
a failure. One morning, after a night of much barbera and noisy
gasconade, old Daniello did not wake up, and two days afterward
they laid him to rest in the sloping graveyard in the gorge by the
olive-oil mill.
Gloomily Armando weighed the situation, standing by the
mullioned window of the room wherein he had toiled so long and
ignobly. Far in the western distance he could see the ships that
seemed to glide with full sails across the mountains. The serene
midsummer vapours, pendulous above the Mediterranean, were
visible, but the sea upon which their shadows fell and lingered was
hidden from his view by a thicket of silver firs. Southward the trees
stood lower, and over their tops, where tired sea gulls circled, he
gazed sadly toward the jumble of masonry that is Genoa.
 Miles below in the sun glare the city lay this morning as Heine
found it decades ago, like the bleached skeleton of some thrown-up
monster of the deep. And a monster it was in the sight of the poor
lad who looked down from the heights of Cardinali—but a monster
that he would conquer, even as Saint George, champion of Genoa,
had conquered the dragon in ages far agone. Yes, he would strike off
for evermore the chains that fettered him to ten-inch Saint Peters,
and mount to the white peaks of art! In the Apennine hamlet he had
lived all his days, and never heard of Balzac; but he clinched his fist,
and, with eyes set upon the cluster of chimney pots at the
mountain’s foot, made his vow:
“In this room, O Genoa! will I bring forth a marble that shall make
you do me honour.”
Then he felt uplifted—as though he had burned the bridges that
hung between his old ignominy and the straight path to fame and
riches. The vow was still fervid and strong within him when, two days
afterward, he beheld in a shop window of Genoa a photograph of
Falguière’s great marble, Juno and the Peacock. Before the divine
contours of Jupiter’s helpmeet the simple-hearted graver of saintly
images stood enchanted. Presently, as though spoken by a keen,
mysterious voice from the upper air, there pierced his consciousness
the word “Replica!” Again and again was it repeated, each time with
a new insistence. Ah, a copy of this in marble! Yes; with such a
masterpiece he would begin his ascent to the white peaks. He
bought the photograph, put it in his pocket and kept it there until he
was beyond the city’s bounds and trudging up the causeway toward
Cardinali. Now and then he took out the picture, regarded it fondly,
and, peering back at the town, asked himself if Genoa would look the
same when his Juno and the Peacock should be there. Would the
soft murmur of that drowsy mass have the same note? Would the
people move with the same pace, eat, sleep, and drink as they had
always done? He was inclined to think they would not.
 Would Genoa be the same when his Juno and Peacock
should be there?

For a twelvemonth, through early tides and late shifts, he

modelled and chipped: in winter, when the demoniac mistral, raging
all about him, shook the workshop and snapped the boughs of the
cypresses; in summer, when the ortolan and the wood-thrush
cheered him with their song. And the little group of neighbours, from
whom he guarded his great artistic secret, marvelled that no more
Saint Peters came forth from their time-honoured birthplace.
Only two persons in Cardinali besides Armando had knowledge
of the momentous affair that was going forward. One was Bertino, a
fair-haired youth of the sculptor’s age, who busied his hands by day
plaiting Lombardian straw into hats, and his head by night dreaming
of America and showering cornucopias of gold. He was Armando’s
bosom friend. The other confidant was Bertino’s foster sister
Marianna, somewhat demure for a mountain lass, and subject to
thinking spells. Beauty she had, notably on feast days, when she
walked to church with a large-rayed comb in her braided chestnut
waterfall, a gorgeous striped apron, and clattering half-sabots,
freshly scraped and polished to a shine. She, too, plaited straw, and
with it wove many love thoughts and sighs for Armando.
At last the stately goddess and her long-tailed companion stood
triumphant in all the candour of marble not wholly spotless. The hour
of unveiling it to the astonished gaze of Bertino and Marianna was
the happiest that the ruler of Armando’s fate permitted him for many
a day thereafter. The bitterness and crushing disillusion came on the
day that he loaded the carved treasure on the donkey cart of
Sebastiano the carrier, and followed Juno and the Peacock down the
mountain pass to the haven of his sweet anticipation.
“He has been saving up his Saint Peters,” said Michele the
Cobbler to a group of mystified neighbours as the cart passed his
shop. “See, he has a box full of them. I wonder how many saints one
can cut out in a year. Ah, well, it was not thus that his uncle Daniello
did, nor his father before him. Shall I tell you what I think, my
friends? Well, I think that boy is going wrong.”
“Ah, si,” was the unanimous voice.
“May your success be great, Armando mine!” said Bertino when
they parted at the first curve of the pass. “Perhaps against your
return I shall have famous news from America. Who knows? Good
fortune be with you. Addio.”
 “The saints be with you to a safe return,” said Marianna. “Addio,
and good fortune.”
“Addio, carissimi amici.”
Sebastiano the carrier lifted the block from the wheel and the
donkey moved on. Armando walked behind, keeping a watchful eye
on the thing in the cart, which was in every shade of the term a
reduced replica of Falguière’s inspiration.
“You must be very careful, Sebastiano,” said he. “Never in your
life have you had such a valuable load on your cart.”
“Bah!” growled the driver. “Valuable! How many have you there?
Are they all the same size? Do you mean to say that I never had a
load as valuable as a boxful of Saint Peters? Oh, bello! Only last
week did I haul a barrel of fine barolo to the Inn of the Fat Calf. Ah,
my dear, that is a wine. Wee-ah! wee-ah!—Go on, you lazy one.
That donkey is too careful.”
They reached their destination in Genoa without mishap. When
the art dealer who had consented to look at it had bestowed on
Armando’s work of a year a momentary survey, he turned to the
sculptor, who stood hat in hand, and regarded him earnestly.
“Who told you to do this, dear young man?” he asked, removing
his eyeglasses.
“Nobody, signore. It was my own idea.”
The merchant turned to Juno with a new interest.
“Not so bad as it might have been,” he shrugged, moving aside to
view the figures in profile. “What is your name? Signor Corrini. Well
—but, my dear young man, it will be a long time, perhaps years,
before you are able to do work of this kind. Naturally, I could not
permit it to remain in my place. What else have you done?
Something smaller, I suppose.”
Armando strove hard to keep them back, but the sobs choked
him.
 While the merchant stood by, offering words meant to comfort,
but which added to his anguish, he replaced the marble in the box
and nailed the lid before rousing Sebastiano from his siesta in the
cart.
“It all comes of keeping the saints too long,” grumbled the carrier,
as he helped lift Juno and the Peacock back into the cart. “Never did
your uncle Daniello have any thrown on his hands—not he. Ah, there
was a man of affairs!”
The donkey tugged at the chain traces, moved the wheels a
spoke or two, then stopped and looked around at the driver, wagging
his grizzled ears in mute but eloquent disapproval of hauling a load
skyward. But after duly weighing the matter, assisted by several
clean-cut hints from a rawhide lash, he set off at his own crablike
pace.
The first turning of the highway attained, Armando paused and
gazed on the city below, his heart aflood with bitterness. Far to the
westward the sun, in variant crimson tones, lay hidden under the
sea, like the last, loftiest dome of some sinking Atlantis. In every
white hamlet of the slopes the Angelus was ringing. Night birds from
Africa wheeled around the towering snares set for them by the
owners of the olive terraces and villas, whose yellow walls in long
stretches bordered the steep route. With his little group of living and
inanimate companions Armando trudged along, his head bowed,
silent as the marble in the cart. The gloaming quiet was unbroken,
save for the gluck of the wheels and the distant chant of the belfries.
They were yet a long way from the outermost cot of Cardinali
when a resounding shout brought the donkey to a standstill and
startled Sebastiano into a “Per Bacco!”
It was the voice of Bertino. He was rounding a curve in the road,
brandishing a piece of folded paper, and clattering toward them as
fast as he could in his heavy wooden shoes. His radiant face
proclaimed that something had happened to fill him with gladness. A
few paces behind came Marianna, but in her eyes there was no
token of joy. She had beheld the loaded cart.
 “Long live my uncle!” cried Bertino, grasping Armando’s hand.
“The letter has come, and I’m off for America. Think of it, Armando
mio, I, Bertino Manconi, going to America! It is no longer a dream. I
am to go—go, do you understand? The money is here, and nothing
can stop me. But come, you do not seem happy to hear of my great
good fortune. I know, dear friend, you are sorry to lose me. Bah! one
can not live in the mountains all his life, and perhaps you too will be
there some day—some day when your Juno is sold. To-night all my
friends shall drink a glass of spumante to my voyage—yes, the real
spumante of Asti. At the Inn of the Fat Calf will I say addio, for I set
sail to-morrow. Tell me, now, do you not count me a lucky devil?”
“You are lucky,” said Armando sadly. “I wish I could go. My own
country does not want me.”
Marianna walked at the tail of the cart. While her brother was
talking she had lifted the box in the hope that it might, after all, be
only the empty one that he was bringing back; but the weight of it
told her the truth she had read in Armando’s face.
“The beast!” she said, “to refuse such a fine thing as that. What
did——”
Armando signalled silence, and pointed to Sebastiano, who
walked ahead. By this time Bertino understood, and he too
exclaimed:
“The beast!”
“Who’s a beast?” asked the muleteer.
“That art merchant, whoever he is. Bah! What would you have?
In this country a fellow has no chance. What a fool one is to stay
here!”
“No, no; the country is good,” said Sebastiano, shaking his head
and jerking a thumb toward Armando. “But what can you expect
when one keeps his Saint Peters a whole year?”
The others exchanged knowing glances and followed on in
silence. The rest of the way it was plain to all who saw Bertino pass
that he was thinking very hard, and with the product of this mental
exertion he was fairly bursting by the time they reached Armando’s
home, for he had not dared to speak in presence of the carrier.
When Juno and the Peacock had been restored to their birthplace he
began:
“Now, listen to me, amici, for I have an idea. I am going to
America. Is not that so?”
“Yes; you are going to America. Well?”
“Patience. You know that as the assistant of my uncle in his great
shop in New York I shall be rather a bigger man than I am here. Who
knows what I may become?”
“Ah, si; who knows?” said Marianna.
“Listen. Now, let us have a thought together. Here is Armando.
He is a fine sculptor. We know that. The proof is here.” He tapped
the big box. “But in Genoa they are too stupid and too poor to buy
his magnificent work. Now, in America people are neither stupid nor
poor. Why can he not make a fortune in America?”
“I can’t go to America,” said Armando.
“No; he can’t go to America,” chimed in Marianna. “What a foolish
idea!”
“Excuse me. Who wants him to go to America? He stays in
Cardinali and makes statues. I go to New York and sell them. Now,
my dears, do you see which way the swallow is flying?”
“But——”
“But——”
“But nothing. Do you think that I, who sail for America to-morrow,
do not know what I am about? Listen. What do you suppose I was
doing on the way up? Well, I was thinking. I have thought it all out. I
ask you this, Armando: Juno and the Peacock you made from a
photograph? Very well; can you not make other things from
photographs? From New York I shall send you the picture of some
great American; some one as great as—as great as——”
“Crespi,” suggested Armando, now interested in the project.
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