Computational Nanotechnology: Modeling and Applications with MATLAB(R)

524 Pages·2012·45.643 MB·English

by  Sarhan M Musa

Nanoscience and Technology
Musa
Computational Nanotechnology
Modeling and Applications with MATLAB®
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Applications of nanotechnology continue to fuel significant innovations in areas
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ranging from electronics, microcomputing, and biotechnology to medicine, consumer d
supplies, aerospace, and energy production. As progress in nanoscale science and
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engineering leads to the continued development of advanced materials and new
lu
devices, improved methods of modeling and simulation are required to achieve a i
n
more robust quantitative understanding of matter at the nanoscale. t
ga
Computational Nanotechnology: Modeling and Applications with MATLAB® t

provides expert insights into current and emerging methods, opportunities, and ai
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challenges associated with the computational techniques involved in nanoscale
n
research. Written by, and for, those working in the interdisciplinary fields that n
d
comprise nanotechnology—including engineering, physics, chemistry, biology, and a
medicine—this book covers a broad spectrum of technical information, research
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ideas, and practical knowledge. It presents an introduction to computational A
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methods in nanotechnology, including a closer look at the theory and modeling p
of two important nanoscale systems: molecular magnets and semiconductor pa
quantum dots.
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Topics covered include: co
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• Modeling of nanoparticles and complex nano and MEMS systems e
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• Theory associated with micromagnetics o
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• Surface modeling of thin films n
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• Computational techniques used to validate hypotheses that may not be
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accessible through traditional experimentation l
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• Simulation methods for various nanotubes and modeling of carbon tg
nanotube and silicon nanowire transistors h
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In regard to applications of computational nanotechnology in biology, contributors M
describe tracking of nanoscale structures in cells, effects of various forces on
cellular behavior, and use of protein-coated gold nanoparticles to better understand A
protein-associated nanomaterials. Emphasizing the importance of MATLAB for
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biological simulations in nanomedicine, this wide-ranging survey of computational
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nanotechnology concludes by discussing future directions in the field, highlighting
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the importance of the algorithms, modeling software, and computational tools in the
development of efficient nanoscale systems. B
®
K11943
ISBN: 978-1-4398-4176-1
90000
9 781439 841761
K11943_COVER_final.indd 1 6/22/11 2:51 PM
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.
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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.