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Nature’s
Nanostructures
Edited by
Amanda S. Barnard & Haibo Guo

Nature’s
Nanostructures

Nature’s
Nanostructures
Edited by
Amanda S. Barnard
Haibo Guo

Published by
Pan Stanford Publishing Pte. Ltd.
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Singapore 038988
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Nature’s Nanostructures
Copyright © 2012 by Pan Stanford Publishing Pte. Ltd.
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ISBN 978-981-4316-82-8 (Hardcover)
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Printed in the USA

Contents
Preface
xv
1. Naturally Occurring Inorganic Nanoparticles:
General Assessment and a Global Budget for
One of Earth’s Last Unexplored Major Geochemical
Components 1
Michael F. Hochella, Jr., Deborah Aruguete, Bojeong Kim,
and Andrew S. Madden
1.1 Introduction 2
1.2 The Nature of Natural Inorganic Nanoparticles:
What Makes Them Special 3
1.2.1 Catalysis by Mineral Nanoparticles 5
1.2.2 Nanomineral Dissolution 7
1.2.3 Sorption by Nanominerals 8
1.3 The Global Distribution and Movement of Naturally
Occurring Inorganic Nanoparticles 10
1.3.1 Volcanoes to Atmosphere 11
1.3.2 Oceans to Atmosphere: Sea Spray Aerosols 13
1.3.3 Continents to Atmosphere: Mineral Dust 14
1.3.4 Atmosphere to Oceans 17
1.3.5 Atmosphere to Continents 19
1.3.6 Ocean Crust to Oceans: Hydrothermal Venting 19
1.3.7 Continents to Shorelines: Rivers 23
1.3.8 Shorelines to Continental Shelves and Slopes 25
1.3.9 Continental Shelves to Open Oceans 26
1.3.10 Continents to Oceans: Glaciers 27
1.4 The Global Budget for Naturally Occurring Inorganic
Nanoparticles 31
Part I Nanominerals and Mineral Nanoparticles 43
2. Uncovering the Physical and Chemical Properties
of Nanominerals and Mineral Nanoparticles 45
R. Lee Penn
2.1 Introduction 45

vi
Contents
2.2 Size of Nanominerals and Mineral Nanoparticles 47
2.3 Characterization 49
2.3.1 High-Resolution Imaging Techniques 51
2.3.2 Compositional Analysis 55
2.3.3 Structure 56
2.3.4 Size 57
2.3.5 Fractionation and Separation 61
2.3.6 Surface Chemistry 62
2.3.7 Mössbauer Spectroscopy and Magnetic
Characterization 62
2.4 Concluding Remarks 63
3. Nanostructures of Natural Iron Oxide Nanoparticles 75
Hiromi Konishi, Huifang Xu, and Haibo Guo
3.1 Introduction 75
3.2 Ferrihydrite Nanomineral 77
3.2.1 Structure, Composition, and Morphology 77
3.2.2 Abiotic Ferrihydrite 80
3.2.3 Biotic Ferrihydrite 81
3.2.4 Extraterrestrial Ferrihydrite 85
3.3 Goethite 86
3.4 Other Iron Oxide Nanoparticles 91
3.4.1 Hematite 91
3.4.2 Magnetite and Maghemite 93
3.4.3 Schwertmannite and Akaganéite 99
3.5 Concluding Remarks 101
4. Thermodynamic Modelling of FeS 2 115
Salvy P. Russo and Andrew Hung
4.1 Introduction 115
4.2 Electronic Structure Calculations of Periodic
and Nanoscale Systems 118
4.3 Thermodynamic Modelling 120
4.3.1 Calculation of Free Energies Using the
Harmonic Approximation 121
4.3.2 Thermodynamic Integration 122

Contents
vii
4.3.3 Shape-Dependent Thermodynamic
Modelling of Nanocrystals 123
4.4 Modelling of Surface Energy for Polar and
Non-Polar Surfaces 124
4.4.1 Modelling Pyrite FeS 2 Surfaces 126
4.5 Modelling of FeS 2 Nanocrystals 130
4.5.1 Shape and Thermodynamic Stability of
FeS 2 Nanocrystals 130
4.5.2 Formation of FeS 2 Nanocrystals in
Sulfur-Rich Conditions 133
4.6 Conclusion 135
5. Noble Metal Nanoparticles in Ore Systems 141
Robert Hough, Martin Reich, and Ryan Noble
5.1 Introduction 141
5.2 Imaging Nanoparticles in Natural Samples 143
5.3 Gold Nanoparticles in Hydrothermal Sulphides 146
5.3.1 “Invisible” Gold in Arsenian Pyrite 147
5.3.2 The Fate of “Invisible” Gold at High
Temperatures 149
5.4 Nanoparticulate Gold and Copper in Supergene
Deposits 151
5.4.1 Gold in Supergene Deposits 152
5.4.1.1 Morphology 152
5.4.1.2 Influence of bacteria 156
5.4.2 Copper Deposits 157
5.4.3 Other Metals 157
5.5 Colloidal Transport 157
5.6 Future Directions 161
6. Diamondoids 169
C. Bostedt, L. Landt, T. Möller, J.E. Dahl, and R.M.K. Carlson
6.1 Introduction and Structure 169
6.2 Diamondoids in the Geosphere 174
6.3 Electronic Structure and Optical Properties 179
6.4 Functionalized Diamondoids 186

viii
Contents
7. Role of Nanopores in Regulating Reactivity and
Transport of Uranium in Subsurface Sediments 195
Huifang Xu and Hun-Bok Jung
7.1 Introduction 195
7.2 Behaviors of Nanopore Surface and Nanopore
Water 200
7.3 Nanopore Surface on U(VI) Sorption and
Desorption in Model Systems 202
7.4 Reduction of U(VI) Sorbed on Nanoporous and
Non-Nanoporous Alumina 204
7.5 Desorption of U-Contaminated Sediments 206
7.6 U(VI) Sorption and Desorption of
Uncontaminated Sediments 209
7.7 Conclusions 216
Part II Biominerals 223
8. Biomineralization of Natural Nanomaterials 225
Jun Wu, Juming Yao, and Yurong Cai
8.1 Introduction 225
8.2 Calcium Phosphate-Based Nano-Biominerals 228
8.3 Calcium Carbonate-Based Nano-Biominerals 234
8.4 Fe-Based Nano-Biominerals 238
8.5 Si-Based Nano-Biominerals 240
8.6 Summary 241
9. Magnetic Nanoparticles in Magnetosomes 249
André Körnig and Damien Faivre
9.1 Introduction 249
9.2 Magnetotactic Bacteria 251
9.3 Magnetosomes 254
9.3.1 Magnetosome Membrane 255
9.3.2 Structure and Composition of
Magnetosome Crystals 256
9.3.3 Morphology of Magnetosome Crystals 257
9.3.4 Dimensions of Magnetosomes 258
9.3.5 Chain Assembly of Magnetosomes 259
9.4 Hierarchical Structuring of Magnetosomes 260
9.5 Application of Nanocrystals and Magnetosomes 261
9.6 Conclusions 262

Contents
ix
10. Nanoscale Magnetoreceptors in Birds 273
Ilia A. Solov’yov and Walter Greiner
10.1 Introduction 273
10.2 Theoretical Methods 275
10.2.1 Micromagnetic Computation 275
10.2.2 Structure Relaxation Procedure 278
10.3 Results and Discussion 279
10.4 Conclusion 286
11. Nucleation and Growth of Biomaterials:
The Role of Simulations for Understanding 295
J.H. Harding, C.L. Freeman, D. Quigley and P.M. Rodger
11.1 Ab initio Calculations and Force-Fields 297
11.2 Simulations and the Nucleation of
Biomaterials 298
11.3 Control of Crystal Growth by Molecules
and Arrays 301
11.4 Aggregation of Nanoparticles and Coarse
Graining 304
11.5 Conclusions and Prospect 305
12. Photonic Crystals in Beetles 313
Ainsley E. Seago and Vinodkumar Saranathan
12.1 Introduction 313
12.2 Photonic Crystals 314
12.2.1 Optics of Photonic Crystals 314
12.2.2 Three-Dimensional Photonic Crystals 315
12.3 Photonic Crystals in Coleoptera 316
12.3.1 Structure and Morphology of Beetle
Photonic Crystals 316
12.3.2 Photonic Crystals in Weevils 317
12.3.3 Photonic Crystals in Longhorn Beetles 317
12.4 Development and Evolution 318
12.4.1 Development of Photonic Crystals in
Coleoptera 318
12.4.2 Evolutionary Origins 319
12.4.3 Adaptive Significance 321
12.5 Summary 322

x
Contents
Part III
Nanoparticles in Space and the
Atmosphere 327
13. Nanoparticles That Are Out of This World 329
Frans J. M. Rietmeijer and Joseph A. Nuth
13.1 Introduction 329
13.2 Grain Coagulation 336
13.3 Vapor Phase Condensation 338
13.3.1 Equilibrium Condensation 338
13.3.2 Non-Equilibrium Condensation 341
13.4 Meteoroids and the Zodiacal Cloud 345
13.4.1 Comet Nuclei 345
13.4.2 Nanoparticles in Meteoroid Streams 346
13.4.2.1 Leonid meteoroids impacting
the Moon 347
13.4.3 The Zodiacal Cloud 348
13.5 Nanograins in the Mesosphere 350
13.5.1 Meteors 350
13.5.2 Mesospheric Metals 350
13.5.3 Meteoric Dust 352
13.6 Nanograins in the Stratosphere 353
13.7 Summary 354
14. Large Molecules and Nanograins in Space 361
A.G.G.M. Tielens
14.1 Nanomaterials in Space 362
14.2 The Temperature of Nanomaterials in Space 370
14.3 Interstellar Nanograins and the Heating of
Interstellar Gas 373
14.4 Evolution of Interstellar Nanomaterials 374
14.5 Summary and Key Questions 380
15. Nanoparticles in the Solar System 385
Ingrid Mann
15.1 Introduction 385
15.2 Dust Measurements from Spacecraft 386
15.3 Nanodust in the Interplanetary Medium 389
15.4 Trajectories of Nanodust in the Solar Wind 390
15.5 Dust in the Upper Earth’s Atmosphere 393
15.6 Future Research 394

Contents
xi
16. Formation and Growth of Atmospheric Aerosol
Particles 399
Tuukka Petäjä, Miikka Dal Maso, Mikko Sipilä, Ilona Riipinen,
Veli-Matti Kerminen, and Markku Kulmala
16.1 Introduction to Atmospheric Aerosols 399
16.2 Atmospheric Aerosol Formation and Growth:
Background and the State of the Art 400
16.3 Observations of Aerosol Formation:
Instrument Development 403
16.3.1 Precursor Gases 403
16.3.2 Atmospheric Ions 404
16.3.3 Aerosol Particles 405
16.4 Laboratory Experiments on Aerosol
Formation 407
16.4.1 Flow Tube Experiments with Acid
and Water 407
16.4.2 Multi-Component Flow Tube
Experiments 408
16.4.3 Chamber Experiments 409
16.5 Atmospheric Observations of Aerosol Formation 411
16.6 Theoretical Understanding of Atmospheric
Nucleation Processes 414
16.7 Parameterization of Atmospheric Aerosol
Formation and Modeling: Its Impacts on
Atmospheric Aerosol Concentrations 416
16.7.1 Nucleation and Aerosol Formation
Parameterizations 416
16.7.2 Modeling the Global and Regional
Atmospheric Aerosol Concentrations 418
16.8 Summary and Future Directions 420
Part IV
Engineered Nanoparticles in the
Environment 441
17. Engineered Nanoparticles and the Environment:
Inadvertently and Intentionally Produced 443
Pratim Biswas, Woo-Jin An, and Wei-Ning Wang
17.1 Introduction 443
17.2 Engineered Nanoparticles: Inadvertently
Produced 445

xii
Contents
17.2.1 Stationary Sources 446
17.2.2 Mobile Sources 450
17.2.3 Bioaerosol Sources 453
17.3 Engineered Nanoparticles: Intentionally
Produced 455
17.3.1 Flame Aerosol Reactor (FLAR) 456
17.3.1.1 Nanoparticle formation in
FLAR 457
17.3.1.2 Film deposition via FLAR 459
17.3.2 Furnace Aerosol Reactor (FuAR) 462
17.3.2.1 Nanoparticle formation in FuAR 462
17.3.2.2 Film deposition via FuAR 464
17.4 Nanotoxicology 465
18. Ultrafine Particles on and Near Roadways 477
Yifang Zhu
18.1 Introduction 477
18.2 Health Effects of Ultrafine Particles 478
18.2.1 Toxicological Studies 478
18.2.2 Epidemiological Studies 479
18.3 Vehicle-Emitted Ultrafine Particles 479
18.4 Spatial Profiles of Ultrafine Particles Near
Roadways 481
18.5 Ultrafine Particles on Freeways 483
18.6 Ultrafine Particle Penetrating Into Indoor
Environments 485
18.7 Ultrafine Particle Penetrating Into In-Cabin 486
18.8 Summary 487
19. Allophane and Imogolite Nanoparticles in Soil and
Their Environmental Applications 493
Guodong Yuan and Shin-Ichiro Wada
19.1 Introduction 493
19.2 Occurrence, Formation, and Characterisation
of Allophane and Imogolite 494
19.3 Surface Properties of Allophane and Imogolite 499
19.4 Environmental Applications of Allophane and
Imogolite 502

Contents
xiii
19.4.1 Adsorption of Cations 502
19.4.2 Interactions With Anions and
Negatively Charged Species 504
19.4.3 Adsorption and Release of Water
and Carbon Dioxide 505
19.4.4 Stabilisation of Soil Carbon 507
19.4.5 Use in Composite Materials 509
19.5 Summary and Perspectives 510
20. Transformation of Engineered Nanostructures in
the Natural Environment 517
Priyanka Bhattacharya, Emppu Salonen, and Pu Chun Ke
20.1 Introduction 518
20.2 Fullerenes Transformed by Phenolic
Compounds 519
20.2.1 C 70 –GA Assembly — An Experimental
Study 520
20.2.2 C 70 –GA Assembly — A Simulation Study 521
20.3 Carbon Nanostructures Transformed by
NOM/Humic Acids 523
20.3.1 Carbon Nanotubes Transformed by
Humic Acids — Experiment 524
20.3.2 Carbon Nanotubes Transformed by
Humic Acids — Simulations 525
20.4 Nanostructures Transformed in Plants 528
20.4.1 Biodistribution of Fullerene–NOM in
Rice Plants 529
20.4.2 Translocation of Fullerene and Fullerol
Across Allium cepa Cells 532
20.5 Quantum Dots Adsorption on Algal
Photosynthesis 537
20.6 Summary 540
Index 545

Preface
Preface
As nanoscience matures into nanotechnology, products containing
nanomaterials are entering our lives. For those of us who work
with nanomaterials professionally, it is an exciting time, filled with
pride and expectation. However, for those outside the research
community, this is a time of change that can be very confronting.
What is nanotechnology, and what impact will it have upon our
lives How do we reconcile with the notion of these new “functional”
pieces of matter that are too small to defect, or avoid. Irrespective
of our perspective, it is both humbling and comforting to realize
nanomaterials are actually not as new as we think, and that Nature
has been producing nanomaterials since the dawn of time. This is a
fascinating realization that inevitably leads to these questions: What
are these natural nanomaterials made of What do they look like
Where can we find them And the most tantalizing, what can they
do
In this book, some of the leading researchers in the world share
their studies of Nature’s nanostructures, and we see that there is
a lot to be learned from the elegant ways that Nature deals with
the complexity of the nanoscale. While we struggle to refine our
laboratory techniques, Nature’s own laboratory has perfected the
production of a range of highly selective nanomaterials. We are
first introduced to this area by Michael F. Hochella and our plenary
authors, who describe a variety of naturally occurring inorganic
nanoparticles, in the context of the general assessment and a
global budget for one of Earth’s last unexplored major geochemical
components.
We follow this introduction with a section dedicated to
inorganic nanostructures produced on Earth (often referred
to as nanominerals), opening with a discussion of physical and
chemical properties of nanominerals by keynote author R. Lee
Penn. This is followed by a detailed account of some of the most
ubiquitous nanoparticles on Earth, iron oxides, which can form in
a variety of different sizes, shape, structures and magnetization
states (depending upon their environment). Of course, the study of

xvi
Preface
nanominerals is not restricted to experimental techniques, and Salvy
Russo and Andrew Hung describe ways that advanced computer
simulation and theoretical modeling can help us determine how to
model and predict how different sizes, shapes, and structures are
formed. We then move on to nanomaterials that are rarer in Nature,
such as gold nanoparticles in ores, described by Robert Hough
and colleagues, and diamondoids extracted from oil, described by
Christoph Bostedt and colleagues. In all of these cases, the natural
nanomaterials have “positive curvature” (that is, they present as
small solid particles); so we conclude this section by considering
the opposite position. The final chapter of this section by Huifang
Xu describes natural nanomaterials with “negative curvature,” and
explains the role of these nanosize pores (or voids) in regulating
reactivity and transport of uranium in subsurface sediments.
Nanomaterials are not the only thing Nature has beaten us to;
Nature has developed its own nanotechnology too. In Part II, we
reveal some of the ways that Nature combines nanoparticles to form
more complex structures, each with a specific application in mind.
The vast majority of these applications are in the realm of biology,
and keynote authors Jun Wu, Juming Yao, and Yurong Cai describe
how our own bodies contain bones with hierarchical structure based
on nanoparticles. We then turn our attention back to iron oxides and
see how the smallest life forms use these magnetic nanoparticles, in
a chapter by André Körnig and Damien Faivre. Bacteria are not the
only life forms to use magnetic nanoparticles, and Ilia A. Solov’yov
and Walter Greiner explain the properties and function of nanoscale
magnetoreceptors in birds. In each case, these nanoparticles have
not been inhaled, ingested or inserted but are formed in situ by
the organism, in an environment that is very different from that of
nanominerals. To understand the formation mechanisms, computer
simulations are again instructive, and John H. Harding and colleagues
explain how modeling the nucleation and growth of biomaterials
to aid in understanding. This section concludes with a chapter by
Ainsley E. Seago and Vinodkumar Saranathan, who focus on some of
Nature’s nanotechnology residing outside the body, in the beautiful
photonic crystals decorating the wings and exoskeletons of beetles.
Both Earth and its inhabitants have lived with (and benefited
from) Nature’s nanostructures for millennia, but as our Part III
keynote authors Frans J. M. Rietmeijer and Joseph A. Nuth show us
that some nanoparticles are “out of this world.” While nanoparticles

Preface
xvii
forming in space are almost certainly well beyond our reach, they are
not beyond our understanding, and we can still learn a lot about the
large molecules and nanograins in interstellar space, as described by
A. G. G. M. Tielens, and those closer to home in our own solar system,
as described by Ingrid Mann. In the final chapter of this section, we
converge still closer to Earth, and Tuukka Petäjä and colleagues
introduce us to the formation and growth of nanoparticles in the
atmosphere, and even the air we breathe.
So as we can see, nanomaterials are all around us: in the Earth,
the air and the heavens. But does that mean that all nanomaterials
behave in these predictable ways Of course not. The majority of
the nanotechnology community is focused on producing an array of
different nanomaterials that do not exist in Nature and do things that
natural nanostructures cannot. These “engineered” nanomaterials
can have very different properties and can respond to the natural
environment in a very different way. However, once these engineered
nanomaterials enter the natural world, they become a permanent
part of it, and as we increase the recyclability and biodegradability
of our products, the probability of this occurring approaches 100
percent.
For this reason, Part IV of this book focuses on the interaction
of manmade nanoparticles with the natural world. At this stage,
these interactions are dominated by inadvertently and intentionally
produced nanomaterials (a consequence of modern life) as
described in our keynote chapter by Pratim Biswas and colleagues.
A more detailed account of the nanoparticles on and near roadways
(which many of us travel on everyday) is then provided by Yifang
Zhu. Guodong Yuan and Shin-Ichiro Wada then discuss allophane
and imogolite nanoparticles in soils and describe the role they play
in environmental remediation and control. We conclude the book
with a study of the interaction and transformation of laboratorysynthesized
engineered nanostructures in the natural environment
by Priyanka Bhattacharya, Emppu Salonen, and Pu Chun Ke, where we
are left to ponder whether Nature will cope with our nanostructures
as well as we have coped with hers.
This book represents the first collection of its type, bringing
together studies from astronomy, physics, chemistry, materials
science, engineering, geology and geophysics, environmental
science, agricultural science, entomology, molecular biology and
health. It would not have been possible without the tireless efforts

xviii
Preface
of all involved, and we would like to thank all the authors for their
wonderful contributions. We would also like to thank Dr. Lin Lai for
his assistance in reviewing the chapters and Yunjing Zhang for her
meticulous help in editing the book.
We hope you enjoy learning all about Nature’s nanostructures.
Amanda S. Barnard
Haibo Guo

“At a time when we are concerned about the potential hazards of engineered nanomaterials,
this book gives a timely and delightful overview of the variety of nanoparticles that exist in
our environment — from noble metal nanoparticles in ore systems and nanodust in the solar
system to magnetic nanoparticles in homing pigeons and photonic crystals in beetles. It is
an enjoyable and a useful companion for anyone interested in knowing about the potential
hazards of nanomaterials and those seeking inspiration from nature to create functional
materials.”
Dr Ai Lin Chun
Senior Editor, Nature Nanotechnology
While humanity strives to synthesize and utilize functional nanomaterials, nature’s own
laboratory has perfected the production of a range of highly selective nanomaterials.
Natural nanomaterials (and even natural nanotechnologies) are all around us, and this
ubiquity inevitably raises questions such as What are these natural nanomaterials made
of Where can we find them What can they do Answering these questions will lead to
a better understanding of the world around us and facilitate new and environmentally
friendly ways of creating and manipulating nanoscale materials for the next generation of
new technologies.
This book represents the first collection of its type and is truly multidisciplinary. The
compilation brings together studies from astronomy, physics, chemistry, materials
science, engineering, geology and geophysics, environmental science, agricultural science,
entomology, molecular biology, and health and is therefore an invaluable resource for
learning how various scientists approach similar problems.
Amanda S. Barnard is leader of the Virtual Nanoscience Laboratory at the
Commonwealth Scientific and Industrial Research Organisation (CSIRO),
Australia’s national science agency. She has a BSc and PhD in physics from
RMIT University, Australia, and has held research positions at Argonne National
Laboratory, USA, and the University of Oxford, UK. Using thermodynamic
theory and first-principles computer simulations, she is a pioneer in the
mapping of nanomorphology and the environmental stability of nanomaterials
(thermodynamic cartography) and in the development of structure/property
relationships for predicting the reliability of nanoparticles in high-performance
applications.
Haibo Guo is a postdoctoral fellow and an early-career researcher at Virtual
Nanoscience Laboratory, led by Dr Amanda Barnard. He received his BS in 2001
and PhD in 2006 from Tsinghua University, Beijing, China. His research interests
include modeling and simulation of surfaces and interfaces in environmental
and energy sciences.
V288
ISBN-13 978-981-4316-82-8
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