AMES LABORATORY A U.S. Department of Energy laboratory operated by Iowa State University

Positive attraction of negative refraction

Better catalysts for biodiesel fuel

Adding to the quasicrystal’s allure

2004 Inquiry

Science and Technology at the Ames Laboratory
(front cover) This wedge-shaped photonic crystal being studied by Ames Laboratory senior physicist Costas Soukoulis was 

designed and constructed as part of a basic research effort to demonstrate negative refraction and superlensing in the microwave 

region of the electromagnetic spectrum. (see story page 2)

(back cover) Glassware hung up to dry make for unusual laboratory artwork.

2 Accentuate the Negative ... Saren Johnston

A combination of theoretical and experimental efforts has led to the demonstration 

of negative refraction in photonic crystals.

6 Stepping Up to Nanoscience ... Saren Johnston

The discovery of a growth mode, never before observed, is providing fundamental 

information about the microscopic processes that control the growth of custommade materials.

9, 24 INtouch 

It’s a busy place – check out a few Ames Lab highlights from the past year.

10 Bioinspired Materials ... Kerry Gibson 

Polymers that respond to changes in temperature and pH are the focus of Ames 

Laboratory chemists who believe these bioinspired materials may one day ease drug 

delivery and gene therapy.

12 Model Behavior for Random Materials ... Kerry Gibson

Ames Laboratory metallurgist Bulent Biner has developed molecular dynamics 

models that may help explain the deformation behavior of metallic glasses. The 

materials seem to have a switch mechanism that kicks in when applied stresses reach 

a certain level.

14 From Farm Field to Fuel Tank ... Steve Karsjen 

Heterogeneous catalysts being developed to produce biodiesel fuel may provide a 

new source of fuel for our nation’s transportation needs and a new market for Iowa 

farmers’ soybeans.

18 Deciphering the Quasicrystal ... Kerry Gibson

Starfi sh and Farey trees are just two phenomena observed by Ames Laboratory 

materials chemists as they seek to unlock the mysteries of the quasicrystal and fi nd 

unexpected order in these aperiodic materials.

22 Toughening Up a Superconductor Toughening Up a Superconductor ... Saren Johnston Saren Johnston

Physicists have found that adding a small amount of carbon to magnesium diboride 

more than doubles the magnetic field the superconductor can withstand.

Contents table of

2

14

18
Inquiry is published annually by the Ames Laboratory Office of 

Public Affairs. Iowa State University operates the Laboratory for 

the U.S. Department of Energy under contract W-7405-Eng-82. 

Located on the ISU campus, the Ames Laboratory is a member of 

the uni ver si ty’s Institute for Physical Research and Technology, a 

network of scientific research centers. 

Editor

Steve Karsjen

Managing Editor

Saren Johnston

Designer

Jan Weedman 

Photographer

Dennis Sailsbury

Student Design 

 Intern

Mina Shin

Copyright 2004 by Ames Lab o ra to ry. 

All rights reserved. For additional 

in for ma tion about Ames Laboratory 

or topics covered in this publication, 

please contact:

Editor, Inquiry

Ames Laboratory

111 TASF

Ames, Iowa 50011-3020

(515) 294-9557

www.ameslab.gov

from the Di rec tor

Welcome to the 2004 issue of Inquiry Inquiry magazine. You’ve caught me magazine. You’ve caught me Wupon returning from a trip to Mexico, combining a chemistry upon returning from a trip to Mexico, combining a chemistry conference and scuba diving. Thus, my guayabera, traditional conference and scuba diving. Thus, my guayabera, traditional 

Mexican attire that has the delightful characteristic of not allowing the use of 

neckties! 

2004 has been a year of rich scientifi c discovery at the Ames Laboratory, 

as is evidenced by the variety of stories in this year’s Inquiry. From 

groundbreaking research in negative refraction in photonic crystals to a 

better understanding of the nanoscale surfaces of quasicrystals to developing 

heterogeneous catalysts for the production of biodiesel fuel, the Ames 

Laboratory continues to perform cutting-edge research that benefi ts the 

Department of Energy and American taxpayers.

In this issue of Inquiry, I invite you to read how physicist Costas Soukoulis 

has confi rmed negative refraction in photonic crystals by building and testing 

a device that when hit by a beam of electromagnetic waves exhibits this 

formerly impossible phenomenon. The research could lead to the creation of 

a “superlens” that would provide superior imaging capabilities for a host of 

medical, environmental and communications technologies. 

Also in this issue, you can read how materials chemist Pat Thiel is using 

scanning tunneling microscopy to examine atomic-scale surface growth of quasicrystals in an effort to better understand how and why 

these crystalline materials form. The results of her research effort may lead to the creation of new nanoscale technologies. 

There’s an old saying, “America runs by truck.” But this won’t be true when we deplete our planet’s stock of oil, so Victor Lin is 

partnering with an Iowa cooperative to develop biodiesel fuel from soybeans. Lin’s research involves the development of heterogeneous 

catalysts that are not only environmentally friendly but could also help lessen the cost to produce biodiesel fuel, creating an even larger 

market for Iowa farmers’ soybean crops.

These stories represent just a smattering of the research you can read about in this issue of Inquiry. I hope you enjoy all the articles.

Adios,
I

t doesn’t happen naturally, but with 

the right kind of man-made materials, 

light can be made to bend, or refract, 

with a negative angle. When light enters 

these specially engineered materials, called 

metamaterials, it takes a sharp turn to the 

left – a negative turn – bending in the 

opposite direction to that seen in natural 

materials. Scientists frequently refer to these 

unique, synthetic materials as left-handed 

materials. 

Metamaterials and the backward-bending 

light they allow are drawing considerable 

attention from physicists because of their 

range of potential applications. Costas 

Soukoulis, an Ames Laboratory senior 

physicist investigating and designing such 

materials, says left-handed materials may 

one day lead to the development of a type 

of flat superlens that operates in the visible 

spectrum. Such a lens would offer superior 

resolution over conventional technology, 

capturing detail much smaller than one 

wavelength of light to vastly improve 

imaging for biomedical and materials 

applications. 

Soukoulis, who is also an Iowa State 

University physics professor, adds that 

another unique property of left-handed 

materials is that they may be fabricated to 

have zero reflectance for all the incident 

angles (those which are hit by the incoming 

electromagnetic waves). It would be difficult 

if not impossible to determine the location 

of an object that does not reflect light, so the 

implications for the development of many 

applications (including a stealth plane coated 

with a metamaterial) are obvious.

Thinking negatively

The development of metamaterials and 

experiments with negative refraction are 

recent efforts, having drawn little serious 

Physicists are latching on to the positive property of negative refraction

 This photonic crystal has a 

negative index of refraction 

equal to -1, providing excellent 

subwavelength resolution. A 

negative index of refraction 

equal to -1 is needed to achieve a 

perfect image.

Accentuate

the Negative

Inquiry 2004

by Saren Johnston

2
3

attention before the late 1990s. However, 

Soukoulis notes that the concept of a 

material with a negative refractive index was 

first put forth in 1968 by Soviet physicist 

Victor Veselago of the Russian Academy of 

Science in Moscow. Veselago envisioned 

materials with a negative refractive index 

within which the electric magnetic 

field and the propagation vector of the 

electromagnetic wave would form a lefthanded triad of vectors – thus the name, 

left-handed materials.

Although Veselago predicted that 

left-handed materials would have some 

unique capabilities, there were no materials 

available on which he could test his 

theories. Thirty years would pass before 

physicists revisited Veselago’s hypothesis 

and began investigating ways to construct 

the type of negative-index material he had 

contemplated decades earlier. But once 

they did, the race was on to construct the 

perfect left-handed material.

Mixed reaction to negative 

refraction

The idea of engineering materials that 

would refract light negatively stirred up 

a fair amount of controversy within the 

scientifi c community. Soukoulis says many 

people regarded the idea with skepticism. 

After all, scientists rely on the principle that 

every naturally occurring material has a 

positive refractive index that measures how 

fast the material transmits light and how the 

light is bent on entering the material. It’s 

fundamental to the fi eld of optics.

In positive refraction, when light, or 

electromagnetic radiation, passes at an angle 

from one material into a different one, 

such as from air into water, it bends to the 

right at the point of entry – the boundary 

between the two materials. Many students 

fi rst encounter the phenomenon of positive 

refraction in high school science class when 

they observe how a pencil placed in a glass 

of water appears distorted, or bent, to the 

right at the point where it meets the water’s 

surface.

Negative refraction reverses this wellestablished confi guration and so met with 

opposition from scientists who believed 

(and some still do) that it wasn’t possible 

to engineer a true left-handed material. 

Such a material would have to include a 

simultaneously negative response to both 

electric fi eld and magnetic fi eld. 

Those questioning the existence of 

negative refraction say it goes against the 

Costas Soukoulis examines one of the 

photonic crystals that was constructed 

to observe negative refraction and 

superlensing in the microwave region of 

the electromagnetic spectrum.

Inquiry 2004

Electric and magnetic fields along with the propagating vector for the 

electromagnetic wave result in a left-handed triad of vectors (E, H, k) for 

left-handed materials and a right-handed triad of vectors (E, H, k) for natural. 

Left-handed Waves Right-handed Waves
4

laws of physics by violating the limit for the 

speed of light. However, in the midst of the 

debate surrounding its existence, proponents 

of negative refraction and Veselago’s 

original thoughts on the subject continue 

to accumulate more and more proof of its 

existence. 

Negative numbers grow

In the late 1990s, other “negative 

thinkers” became intrigued with Veselago’s 

ideas on negative refraction. John Pendry 

of Imperial College in London determined 

that although negative index materials 

don’t exist in nature, it might be possible 

to design and construct such materials. 

Pendry and members of his research group 

were able to create a synthetic material 

that showed a negative response to electric 

fi eld. They quickly followed up on that 

success by building a second synthetic 

material that showed a negative response to 

magnetic fi eld. That left the challenge of 

combining those properties to create the fi rst 

metamaterial.

Soukoulis’ colleague, David R. Smith of 

the University of California at San Diego, 

met the challenge. Smith and his research 

team were the fi rst to construct and test a 

material that exhibited a negative response 

to both electric fi eld and magnetic fi eld in 

the microwave region of the electromagnetic 

spectrum. Their metamaterial consisted of 

small copper loops and wires and showed 

that microwaves passing through the 

material were negatively refracted.

Moving down the spectrum

Researchers are just beginning to explore 

applications for negative refraction at 

microwave frequencies – and there are 

many. But even as that work gets underway, 

some physicists are looking down the 

electromagnetic spectrum and focusing their 

attention on visible light. Soukoulis and 

members of his research team are leaders in 

that effort. He emphasizes that a material 

with a negative refractive index for visible 

light would bring about a remarkable 

transformation in science and technology.

Unlike natural materials, metamaterials 

can focus light without the need for 

curved surfaces. Soukoulis says this 

characteristic would allow a fl at piece of 

a metamaterial for visible light to serve 

as a superlens – one capable of focusing 

electromagnetic radiation to atomic scale 

length. Potential applications for such a 

lens include superior imaging for medical 

and biomedical diagnostics, monitoring 

air quality, detecting dangerous substances 

and making it possible to etch ever-smaller 

electronic devices for cellular and optical 

communications.

The negative promise of 

photonic crystals

With the success of constructing 

metamaterials for microwave frequencies 

and the desire to create a technologyaltering superlens has come an inspired 

effort by physicists to develop a negative 

refractive index material for visible light. 

Working toward that goal, Soukoulis and 

his research team have been investigating 

photonic-bandgap crystals, man-made 

materials that can transmit wavelengths 

of light up and down the electromagnetic 

spectrum and so have alternating regions 

of different refractive indices. The 

materials are like old friends to Soukoulis, 

who collaborated with Ames Laboratory 

researchers Kai-Ming Ho and Che-Ting 

Chan in 1990 to theoretically demonstrate 

the existence of the fi rst PBG crystal.

Working with his colleagues at Ames 

Laboratory and at the FORTH research 

center in Greece, Soukoulis has done 

the calculations and developed the fi rst 

computer simulations that show negative 

refraction in a two-dimensional, lefthanded photonic crystal. Photonic crystals 

are periodic structures made from dielectric 

materials – materials that are electrical 

insulators or in which an electric fi eld can 

be perpetuated with a minimum loss in 

power.

The photonic crystal metamaterial 

Soukoulis and his collaborator, Ekmel 

Ozbay, at Bilkent University in Ankara, 

Turkey, designed and tested consists of a 

square array of alumina rods at which the 

researchers aimed a beam of microwaves 

to demonstrate negative refraction and 

superlensing in the microwave region of the 

electromagnetic spectrum. 

In addition to showing that the 

incoming beam is negatively refracted, the 

simulations revealed another signifi cant 

piece of information. Refraction does 

not occur immediately. The incoming 

electromagnetic wave is temporarily delayed 

and trapped at the boundary between 

the air and the negative refractive index 

photonic crystal before it eventually moves 

in a negative direction.

Soukoulis and his colleagues maintain 

that the outer rays in the delayed beam 

give the impression of traveling faster than 

the speed of light because of this trapping 

mechanism. Pendry, who performed much 

of the early research on negative index 

materials, notes that the calculations and 

simulations done by Soukoulis’ team are 

“important confi rmation that the speed of 

light is not violated by negative refraction.” 

Soukoulis says, “The negative refraction 

effect we’ve demonstrated depends only 

This metamaterial exhibits the properties required for negative 

refraction: negative electric permittivity, negative permeability 

and negative index of refraction.

Inquiry 2004
Lei Zhang adjusts a photonic crystal for angle and transmission 

measurements.

Based on the calculations and simulations done by Soukoulis, 

experimentalists working on the left-handed materials team are 

constructing metamaterials and photonic crystals to observe negative 

refraction. Lei Zhang, an Ames Laboratory graduate assistant working with 

Soukoulis, carries out many of these experiments under the supervision of Gary 

Tuttle, an Ames Laboratory associate working at ISU’s Microelectronics Research 

Center. The MRC is a member center of the university’s Institute for Physical 

Research and Technology.

Zhang’s experiments with metallic structures built to conform to Soukoulis’ 

simulations support his theoretical results for the microwave region of the 

electromagnetic spectrum. The metamaterials exhibit the properties associated 

with negative refraction – negative electric permittivity, negative permeability and 

negative index of refraction – the combination of which can exist only in synthetic 

devices.

Zhang’s photonic crystal experiments confirm what Soukoulis predicted: 

negative refraction and superlensing can be observed in photonic crystals in the 

microwave region. The next step will be to adapt the technology to other regions of 

the electromagnetic spectrum, with the ultimate goal of reaching the visual region. 

However, achieving that goal will require the expertise to fabricate the photonic 

structures at extremely small length scales. Zhang suspects that objective may be 

a distant one. For now, she says she would be thrilled to create a successful lefthanded material closer to the infrared region of the electromagnetic spectrum.

5

on the refractive index of the dielectric 

material making up the photonic crystal and 

the geometric factors of two-dimensional 

photonic crystals. Therefore, this effect can 

also be observed at optical wavelengths by 

using transparent semiconductors to obtain 

similar refractive indices.”

Soukoulis’ work moves physicists one 

step closer to constructing materials that 

exhibit negative refraction at optical 

wavelengths and realizing the much-soughtafter superlens. But, as he says, there is still 

much to be done. “We want to know more 

about what happens when electromagnetic 

waves are directed at a negative index 

photonic crystal – what causes the delay in 

the instant before the wave is refracted,” he 

says.

Soukoulis will also continue to work 

on new designs for 2-D and 3-D negativerefractive-index photonic crystals, and part 

of that effort will be to resolve the energy 

losses that become larger and larger with 

the move to higher frequencies in the 

electromagnetic spectrum. “Discovering the 

origin of these losses – that’s the theoretical 

challenge,” he says.

For more information:

Costas Soukoulis, (515) 294-2816

soukoulis@ameslab.gov

Research funded by:

DOE Offi ce of Basic Energy Sciences,

 Materials Science and Engineering 

 Division

Department of Defense

 Defense Advanced Research Projects 

 Agency

Inquiry 2004
6

Advertisers tout them, consumers 

clamor for them, and 

manufacturers scramble to meet 

consumer demand. What causes all this 

hoopla?

It’s the need or desire, or both, 

to have the latest-and-greatest, most 

technologically advanced version of just 

about anything.

However, the most up-to-date version 

of a product debuts only after substantial 

groundwork has been laid. In reality, we 

owe the availability of new and improved 

technologies that make our lives easier to 

a lot of hard work at the research bench. 

That’s where fundamental science takes 

place, where researchers study materials 

and their properties with the goal of 

developing new materials with better 

properties.

Everything we see, use or produce 

– from cookware to computer chips – is 

made from materials, which are, in turn, 

made up of atoms. How the atoms are 

arranged in a material determines the kind 

of properties exhibited by that material and 

ultimately by the products made from it. 

At Ames Laboratory, senior physicist 

Michael C. Tringides is involved in a basic 

research effort to broaden the knowledge 

base about materials and their properties. 

He and members of his research group, 

Unusual growth mode leads to more control 

over atomic-scale structures

 “Stepping” up to

Nanoscience 

The scanning tunneling microscopy, 

or STM, image above clearly reveals 

the uniform height and self-organized 

growth of the PbSi(111) islands studied 

by Michael Tringides and members of 

his research group. The majority of the 

islands are seven layers high.

Inquiry 2004

by Saren Johnston
7

associate scientist Myron Hupalo and 

graduate students Vincent Yeh and 

Michael Yakes, focus their efforts on the 

microscopic processes that control the 

growth of custom-made materials.

“Control is the name of the game,” says 

Tringides, talking about the importance 

of growing atomic structures in uniform 

sizes and with highly ordered geometries 

for potential applications that include 

sensors, switches, lasing materials and 

semiconductors that allow computer chips 

to run faster.

Exciting as the potential is for the 

development of these nanotechnologies 

(artifi cially fabricated structures in 

the nanometer range of 0.1-100 nm) 

and other microminiature equipment, 

Tringides is acutely aware of the long 

hours of fundamental research required to 

bring them about. The work he and his 

colleagues pursue may prove critical in the 

further miniaturization of silicon-based 

electronic devices, a major undertaking in 

light of the silicon industry’s huge role in 

technological innovation and production.

Manipulating miniatures

Tringides explains that vital to the 

success of these miniaturization efforts is 

the ability to achieve exact control of layer 

thickness and atomic uniformity of thin 

fi lms and nanostructures – what he refers 

to as “the ‘Holy Grail’ in nanotechnology, 

the next major industrial revolution.”

Noting the great demand for these 

materials within the silicon industry, 

Tringides says, “It’s essential that these 

structures are grown in a robust and 

reproducible way, with easy size selection. 

Contrary to conventional wisdom, we’ve 

discovered that an intriguing type of 

self-organization is possible with lead 

(Pb) deposited on silicon (Si) if the 

Michael Tringides and his research group are seeking what he says is the 

“Holy Grail” in nanotechnology – gaining control of layer thickness and atomic 

uniformity of thin fi lms and nanostructures. (clockwise, from lower left: 

Tringides, Vincent Yeh, Michael Yakes and Myron Hupalo)

growth is carried out at low temperature 

– around 185 Kelvin, or minus 126 degrees 

Fahrenheit.” He adds that in all other 

systems studied so far, the deposited metal 

atoms stack up in islands of very different 

height variation. But for Pb grown on Si 

(oriented along the (111) crystal axis), he 

says the atoms seem to be “intelligent” and 

make only one height choice.

“The selected height of these 

nanostructures is related to their electronic 

structure,” Tringides continues. He 

explains that keeping electrons confi ned 

in small metal islands requires them to 

occupy sharp energy levels as dictated by 

the laws of quantum mechanics. This 

confi nement implies that the total energy 

of the electrons depends strongly on the 

nanostructure’s size or shape. “This is 

called Quantum Size Effects, or QSE,” 

says Tringides, “and a consequence of this 

relationship is that certain fi lm thicknesses 

are more stable than others.”

Tringides is able to grow Pb islands of 

fi ve layers by using a different type of 

silicon surface as the substrate.

Inquiry 2004
8

Electron diffraction “fringes” (similar 

to the ones formed when light scatters 

from a very thin air wedge, but of 

much larger size) can be used to 

deduce that practically all islands are 

seven layers high for lead coverages 

between 2.5 ML, or monolayers, 

and 7.5 ML.

Charting new islands

Tringides and his research group were 

the fi rst to observe and monitor the highly 

unusual formation of uniform-height 

Pb/Si islands. They observed the 7-step 

(or 7-layer), steep-edged, fl at-top islands 

using two complementary techniques. 

Quantitative electron diffraction, used by 

Yeh and Yakes, samples the island height 

uniformity by refl ecting electron waves 

from the surface. Scanning tunneling 

microscopy, or STM, allows scientists 

to see the structure of the islands with 

atomic resolution. STM, used primarily 

by Hupalo, images the islands and gives 

the island size and shape directly, without 

further data analysis. “As a result of our 

investigations, we have shown that not 

only can QSE be observed in small objects, 

but QSE can dictate the island uniformity 

and height,” says Hupalo.

The scientists were amazed to see this 

uncommon growth mode of the 7-step 

Pb islands, which clearly shows that the 

deposited atoms seem able to “climb” and 

select preferred, fi nal positions. “No one 

was expecting to see the uniform-height, 

self-organized growth,” says Tringides. 

“We couldn’t believe how quickly the 

islands formed following deposition. 

Nature, itself, was doing the work for us!”

Taking control

Tringides explains that although QSE is 

the driving force for height uniformity, one 

still needs to fi nd the right temperature 

and surface coverage conditions for the 

islands to form. These variables make it 

diffi cult to predict when the self-organized 

growth is possible and explain why it has 

never been seen before.

“It’s necessary to study the growth 

as a function of the different growth 

parameters, such as temperature and 

deposition rate, to discover when such 

self-organized nanostructures form,” says 

Tringides. By varying these parameters in 

the Pb/Si(111) system, he and his coworkers found that only odd island heights, 

i.e. 5, 7, and 9 layers, are possible. Using 

these growth parameters, they developed a 

kinetic phase diagram that serves as a guide 

to select the desired island height.

But Tringides warns that island height 

uniformity exists only at suffi ciently low 

temperature. At higher temperature, 

the islands evolve into multiheight 

mounds, limiting their potential for 

room-temperature applications. Working 

to resolve the problem, Tringides and 

members of his research group have 

discovered that they can “manipulate 

the growth” by adsorbing oxygen, which 

restricts the upward motion of the Pb 

atoms, allowing the islands to maintain 

the same height at higher temperatures. 

This process extends their potential 

for technological applications. “At the 

same time, it raises important theoretical 

questions about how the potential energy 

surface of the Pb islands is modifi ed by 

oxygen adsorption,” Tringides says.

For more information:

Michael Tringides, (515) 294-6439 

tringides@ameslab.gov

Research funded by:

DOE Offi ce of Basic Energy Sciences,

 Materials Science and Engineering 

 Division

Inquiry 2004
Intouch

9

“Powering Up”

An identical SUR grant was also awarded to Ken Jordan, a 

colleague of Gordon’s at the University of Pittsburgh. “This 

is intended to be the fi rst stage in what IBM calls a strategic 

partnership between Iowa State and Pittsburgh,” says Gordon. “A 

potential aspect of the partnership is a joint postdoctoral position 

with IBM. That means IBM might fund half of a postdoc position, 

and I would fund the other half.” Gordon says that individual 

would spend most of the time in Ames, but part of the time doing 

life-science-related research for IBM at the Maui High Performance 

Computing Center in Hawaii.

“The Maui Center is mostly funded by the Department of 

Energy,” says Gordon. “It’s an IBM shop – all of their computers 

are IBMs.” 

According to Gordon, the initial target of the life sciences 

research will be to learn more about water. “We’re developing 

models that will provide accurate calculations on water molecules, 

from very small numbers of water molecules to very large numbers,” 

he says. The work will make it possible to simulate both the 

molecular properties and the macroscopic properties of water 

molecules.

“All of the biological processes in living things occur in water, so 

the fi rst step in really being able to simulate those processes is to do 

very good calculations on water,” explains Gordon. “The next step 

is to look at the processes that are occurring in the water.”

Pittsburgh’s Jordan, Gordon’s SUR grant partner, is also very 

interested in water clusters. “He uses the models created by other 

researchers and develops simulation programs,” says Gordon. “It’s 

actually a very nice fi t because we’ll do all the models that he’ll use. 

The partnership will allow for a lot of good interactions.”

2004

IBM grant 

will increase computer power 

for Ames Laboratory and ISU

Inquiry 2004

by Saren Johnston

Brett Bode, associate scientist in the Ames Laboratory’s 

Scalable Computing Lab, examines one of the three IBM Power 

4 workstations that came to Ames Laboratory and Iowa State 

University through a Shared University Research grant. Each 

workstation contains eight central processing units for a total of 24 

CPUs that will greatly enhance the SCL’s parallel computing power. 

Massively parallel power just got a boost at Ames 

Laboratory and Iowa State University with the 

awarding of an IBM Shared University Research 

Grant to Mark Gordon. This is the third SUR grant awarded 

to Gordon, program director of Applied Mathematics and 

Computational Sciences and an Iowa State University distinguished 

professor of chemistry. The grant’s primary focus is life sciences 

research.

“Very few SURs were approved for funding – ours and one or 

two others – so we were very high priority,” says Gordon. “Jamie 

Coffi n, my contact at IBM and their vice president of Health Care 

and Life Sciences Industry, was very instrumental in our selection,” 

he adds. 

The SUR grant came through the ISU Foundation to 

Gordon’s chemistry research group in the form of three IBM 

Power 4 computer workstations. The workstations are valued at 

approximately $434,000 according to Amy Brockhorn, IBM client 

executive for Iowa State.

IBM certifi ed pSeries specialist Julie Cray says the three Power 

4 workstations, together, contain 24 central processing units, 96 

gigabytes of memory, 876 gigabytes of disk space, and 111,870 

megafl ops of operating power – all of which will substantially 

increase parallel computing power in Ames Laboratory’s Scalable 

Computing Lab. Computational scientists in the SCL will 

confi gure the workstations into a “cluster” to create a 24-node 

parallel computer.
10 

CREATING POLYMERS

Even the simplest organisms 

contain “magical” substances, such 

as proteins, lipids, and DNA, that 

react to chemical and environmental cues to 

perform a variety of tasks from controlling 

chemical balances to regulating growth and 

cell reproduction. 

Researchers at Ames Laboratory are 

studying a group of bioinspired, selfassembling polymers to understand how 

they are able to form and react to stimuli 

similar to the way proteins, lipids and 

DNA react in nature. Unlocking how these 

soluble block polymers are able to selfassemble could potentially lead to a variety 

of uses, such as controlled release systems 

for sustained and modulated delivery of 

drugs or gene therapies.

THAT ACT LIKE PROTEINS

 by Kerry Gibson

Inquiry 2004

Materials chemist Surya 

Mallapragada looks at selfassembling block polymers through 

a cryotransmission microscope.

Ames Laboratory researchers are studying self-assembling polymers
11

Pentablock polymers

Ames Laboratory materials chemist Surya 

Mallapragada and her research team are 

focusing on pentablock polymers – 

polymers that form in strings of fi ve chains. 

Each string is comprised of two cationic 

(positively charged) blocks, two hydrophilic 

(water loving) blocks, and one hydrophobic 

block. Because the hydrophobic block tries 

to avoid water, it forms the center of the 

string, with the hydrophilic next and the 

cationic blocks on the outside. In solution, 

these strings form in small clusters called 

micelles, again with the hydrophobic blocks 

at the center.

“The interesting thing about these 

polymers is that they respond to changes in 

temperature and pH,” says Mallapragada, 

who is also an Iowa State University 

associate professor of chemical engineering. 

“As the temperature goes up, the micelles 

cluster together more, forming a polymer 

gel. A similar reaction takes place as pH 

rises – the hydrophobicity of the cationic 

blocks increases, which also helps in gel 

formation.”

Temp and pH sensitive

As temperature and/or pH drops, the 

process reverses itself, and the gels dissolve 

back into micelles and polymer strands. 

Using cryotransmission electron microscopy, 

Mallapragada’s group is working to 

understand just how these micelles look and 

how fast the polymers respond to changes in 

temperature and pH.

“Samples are plunged into liquid 

ethane, which freezes them so quickly that 

ice doesn’t form and disrupt the crystal 

structure,” she says. “We’re able to then 

view the gel formation at various stages 

(temperature and pH) under very controlled 

conditions.” She adds that this work will 

be complemented by conducting X-ray 

scattering studies at the Advanced Photon 

Source facility at the Department of 

Energy’s Argonne National Laboratory.

The structure appears to be the key in 

how the polymers react to stimuli similar 

to the way biomolecules react in nature. 

These substances carry out a wide variety 

of tasks, responding to subtle changes in 

body chemistry regulating those changes. 

The problem in working with proteins 

and similar biomolecules, according to 

Mallapragada, is that it is diffi cult to isolate 

the materials without damaging them.

“Biomolecules often exist in extremely 

small quantities,” she says, “and are not very 

robust. In separating them from a source, 

they become denatured, or damaged. The 

polymers we are studying are much more 

stable, readily available and therefore easier 

to study.”

Delivery potential

Because they are easier to work with, 

the polymers could potentially be modifi ed 

and used as a way to deliver drugs or gene 

therapies. For example, incorporating the 

glucose-oxidase enzyme in the polymer 

would make it sensitive to changes in 

glucose levels in the body. Soluble at room 

temperature, the polymer could be injected 

under the skin where it would form in a 

gel due to the higher temperature of the 

Inquiry 2004

body. When the gluconic acid level falls, 

the resulting drop in pH would cause the 

polymer to swell and release insulin.

The injectable gels would be much 

less invasive than surgically implanting 

automatic insulin delivery systems, and the 

gels would dissolve on their own after about 

a week.

For potential gene therapies, the 

positively charged (cationic blocks) 

polymers can complex with DNA 

(negatively charged). The polymers 

could be used to deliver so-called suicide 

genes and chemotherapy drugs directly 

and selectively to tumors, since normal 

cells would be less likely to react with the 

polymer and express the incorporated gene.

A preliminary in vivo study in 

rats, funded by an ISU Bailey Career 

Development Grant, is now underway in 

conjunction with the John Stoddard Cancer 

Center at Iowa Methodist Medical Center 

in Des Moines.

For more information:

Surya Mallapragada, (515) 294-3645

suryakm@iastate.edu

Research funded by:

DOE Offi ce of Basic Energy Sciences

 Materials Chemistry Division 

This schematic shows how clusters, or micelles, of polymer strings group 

together as the temperature rises (center) and then respond to changes in pH 

(right). Each string is comprised of fi ve blocks – one hydrophobic block (blue), two 

hydrophilic blocks (red) and two cationic blocks (green).
12 Inquiry 2004

by Kerry Gibson

S

ince the 1960s, scientists have 

marveled over amorphous metal 

alloys, materials also known as 

metallic glass, for their unique physical, 

and sometimes electrical and magnetic, 

properties. Now researchers at Ames 

Laboratory are closer to answering how 

these materials are able to take on certain 

high-strength and elastic properties that 

stem from their “glassy” origins. 

Metallic glass can be formed in 

various ways, but the most common is by 

quenching a molten metal alloy so quickly 

that its normal crystalline structure doesn’t 

have a chance to form. Instead, the atoms 

are randomly scattered along with empty 

regions, so-called free volume. This lack of 

crystalline structure gives metallic glasses 

high-strength, elastic properties that make 

them more rigid than ordinary metals/

alloys. These good mechanical properties 

are accompanied by very low ductility at 

room temperature. Yet by heating metallic 

glasses to a few hundred degrees Centigrade 

– but still below their melting points – they 

can be formed into very complex shapes.

It’s these deformation behaviors that 

Ames Lab metallurgist Bulent Biner is 

seeking to explain. 

ODEL BEHAVIOR

Random Materials

for 

Metallurgist Bulent Biner sits next to the powerful 

computer cluster used to generate his molecular 

dynamics simulations of the deformation behavior of 

metallic glasses.
13 Inquiry 2004

This graphic representation shows the evolution of microstructure with time 

during deformation under constant stress. Atoms were colored depending 

on the strain they accumulated, and arrows indicate the location of the free 

volumes as observed during the MD simulations.

Flipping a switch?

 “These materials seem to have a 

switch mechanism near their transition 

temperature,” says Biner, who is developing 

molecular dynamics simulations to 

try to explain these peculiar materials. 

“At lower temperatures, when stress 

is applied, the deformation that takes 

place is inhomogeneous — small clusters 

of randomly packed atoms appear to 

work in concert to form so-called shear 

transformation zones.

“These zones localize displacements 

in surrounding regions that trigger the 

formation of highly localized shear bands 

during the deformation,” Biner continues. 

“In other words, the deformation spreads 

out from these zones as we see in granular 

materials like sand.”

As temperatures approach a metallic 

glass’ transition temperature, however, 

the deformation is no longer localized 

and becomes uniform. Individual atomic 

jumps are the basic step in the mechanism 

of this homogenous deformation. In order 

for individual atomic jumping events to 

take place, there should be enough free 

volume (open space) in the immediate 

neighborhood to accommodate the volume 

of the jumping atom.

Furthermore, the applied stresses may 

cause additional creation of free volume by 

squeezing the atoms into a smaller available 

free volume by displacing the surrounding 

neighboring atoms. However, this extracreated free volume is quickly distributed 

among the neighboring atoms by local 

rearrangement, a process called annihilation.

Excess Free Volume

The fascinating thing Biner has observed 

in computer simulations is that as the stress 

on the materials is increased, the material 

reaches a point where it can’t deform fast 

enough to annihilate the free volume 

created, which helps explain how the 

material goes from elastic to plastic to its 

breaking point with the accelerated rate of 

deformation.

“The main switch mechanism seems 

to be the free volume,” he says. “What 

happens in the low stress region is you are 

creating free volume but it’s annihilated 

away – there’s no excess. In a way, the 

deformation keeps up. When you move to 

the higher stress region, excess free volume 

is created and it becomes like a sponge with 

lots of voids, and then it fi nally breaks.” 

To model this behavior, Biner uses a 

two-dimensional binary system – “to keep 

things simple” – with a ratio of .81 between 

the two atom types. However, even with 

a “simple” system, the computations 

necessary to generate the simulations require 

a signifi cant amount of computer power 

and execution times of many days, even 

when carried out on the powerful clusters 

of computers in Iowa State University’s 

physics and astronomy department. The 

model system was subjected to constant 

stress levels, ranging from 0.1 to 0.45 

micro-pascals and the axial strain calculated 

over time. To view computer-generated 

molecular dynamics simulations of the 

deformation in progress, go to the Materials 

and Engineering Physics Web site at

http://www.metcer.ameslab.gov/research/

amorphous/aahighlights.html. 

These values were then used to generate 

additional data, all of which closely matches 

the experimental data generated by Ames 

Laboratory scientists Dan Sordelet and 

Matt Kramer in their studies of these 

extraordinary materials. The apparent 

match of theoretical and experimental brings 

the researchers closer to understanding these 

unqiue materials, and that’s what makes the 

effort worthwhile for Biner.

“In the long run, that’s what we’re trying 

to understand – how the free volume 

evolves by the atomic arrangements and 

hopefully allows us to make a better 

system,” Biner says.

For more information:

Bulent Biner, (515) 294-0770

biner@ameslab.gov

Research funded by:

DOE Offi ce of Basic Energy Sciences, 

 Materials Science and Engineering Divison
14

to Fuel Tank

A person need look no further than 

articles in their local newspaper to A know that something needs to be know that something needs to be w that something needs to be 

done to help curb our nation’s dependence 

on domestic and foreign oil. Elevated prices 

have made any type of major diesel-fuel users, 

whether they be farmers, fleet managers or 

municipalities, painfully aware of the necessity 

of finding alternative fuel sources. And where 

better to look for these sources than Iowa’s 

farm fields. As a national leader in soybean 

production, with crop projections of over 350 

million bushels in 2003, Iowa’s soybean farmers 

stand to make an enormous contribution to 

our nation’s energy independence.

Biodiesel gains attention 

as an alternative fuel source

From Farm Field

Inquiry 2004

Photo courtesy of USDA Natural Resources Conservation Service

by Steve Karsjen
15

Soydiesel, or biodiesel, is one of the 

products gaining favor as an alternative fuel 

because it’s clean burning and biodegradable 

and can be made from a renewable resource, 

in this case, soybeans. It’s also being eyed as 

a more environmentally friendly industrial 

solvent that could be used for the removal 

of graffi ti or for cleaning up oil spills. But 

there are several keys to making soydiesel 

more attractive as a fuel – some related to 

the fact that industry is not geared up to 

produce biodiesel on a large scale. Other 

more signifi cant issues relate to the costs 

of producing it and disposing of the wastes 

created by the production process. 

The effort to discover more effi cient 

catalysts got its start with the help of a 

Science with Practice grant from the Iowa 

State University Center for Catalysis and the 

Ames Laboratory Biorenewable Resources 

Consortium. The successful results of 

that research led to the awarding of a $1.2 

million grant from the U.S. Department of 

Energy and U.S. Department of Agriculture, 

which will be used to study new technologies 

for production of methyl ester, or biodiesel, 

from soybeans. 

“Our new technology has the potential 

to reduce energy consumption, enhance 

economic competitiveness and lower the 

environmental imprint of methyl ester 

production,” says George Kraus, director 

of the BRC and the CCAT, and an ISU 

professor of chemistry. 

Catalysts are key to converting 

triglycerides like soybean oil to biodiesel. 

To create biodiesel from soy oil, scientists 

perform a chemical reaction whereby they 

replace the glycerol in the oil with methanol. 

This process requires the use of a catalyst. 

Catalysts are used to speed up the rates of 

chemical reactions without getting used up 

in those reactions themselves. The current 

process to convert soy oil into soydiesel relies 

on the use of homogeneous catalysts. The 

process, called transesterifi cation, replaces 

one ester in the soy oil with another to 

create biodiesel. 

But there are problems with using 

homogeneous catalysts to manufacture 

soydiesel. In the example just mentioned, 

sodium methylate is the preferred 

homogenous catalyst. It mixes with 

methanol and soybean oil to create biodiesel. 

Because it is a strong caustic and corrosive 

base, the remaining sodium methylate in the 

biodiesel product mixture cannot be reused 

and must be neutralized with an acid, which 

adds unwanted expense to the biodiesel 

production process. 

Also in the mix, is an expensive wastestorage problem because homogeneous 

catalysts are not easily recyclable. In 

Victor Lin adds some heterogeneous catalyst to soybean oil to create biodiesel. 

Inquiry 2004
16

addition, the time it takes to do all of 

this is another factor. When combined, 

these issues make biodiesel production less 

fi nancially attractive to producers, like West 

Central Cooperative of Ralston, Iowa. West 

Central is a large, farmer-owned cooperative 

in west central Iowa that annually processes 

approximately 72 million pounds of soy 

oil into biodiesel. West Central sells this 

product to distributors nationwide. 

“The success of biodiesel all comes down 

to costs,” says Myron Danzer, sales and 

production manager for West Central. And 

like any business, West Central wants to 

keep costs down and profi ts high. Doing so 

will require reducing the costs to produce 

biodiesel and eliminating the waste problem 

that comes with using homogeneous 

catalysts in the transesterifi cation process. 

The solution to both problems could 

lie in the development of heterogeneous 

catalysts. Because heterogeneous catalysts 

can be easily separated from the product by 

fi ltration, using them eliminates the expense 

of having to add acid to the biodiesel 

production mix. Also, in contrast to the 

nonrecyclable homogeneous catalysts, the 

heterogeneous catalysts can be reused many 

times, which further lowers the cost of the 

biodiesel production. 

To fi nd someone doing research in the 

area of heterogeneous catalysts, West Central 

had to travel only about 60 miles up the 

road to the Ames Laboratory and Iowa State 

University. Catalysis is currently a research 

thrust of the Ames Lab’s Biorenewable 

Resources Consortium and Victor Lin, an 

Ames Lab chemist and an ISU assistant 

professor of chemistry. Lin’s research is in 

the production of heterogeneous catalysts. 

Through the DOE/USDA grant, Lin and 

West Central are collaborating to scale up 

production of test heterogeneous catalysts, 

analyze tests and design equipment to mass 

produce new catalysts. 

The effort to design a more effi cient 

biodiesel conversion process revolves around 

Lin’s work in the area of “mesoporous 

silica nanocatalysts.” These honeycombed 

particles speed up the conversion process 

and can be more easily separated and 

recycled after they’ve done their job. 

“If we can replace the homogeneous 

catalyst with one that’s heterogeneous, it 

would allow us to isolate the catalyst and 

also recycle it so we don’t have to waste 

time and effort trying to neutralize the base 

catalyst with the acid,” says Lin. 

Free Fatty Acids

Creating biodiesel from soybeans is 

just one chapter of the story for Ames 

Laboratory and West Central. The 

cooperative would like to expand the variety 

of products it uses as feedstock to produce 

biodiesel. One of the items at the top of the 

list of potential “other” materials is corn. 

Iowa farmers harvested around 1.87 billion 

bushels of corn in 2003, so the potential 

exists for a major market for this product. 

Other feedstocks also on the list are 

poultry fat and waste grease. “We want the 

capability of using what they call multiple 

feedstock,” says Danzer. 

Unfortunately, these feedstocks are more 

expensive to turn into biodiesel than soy oil 

because they contain a small amount of free 

fatty acid, or FFA. Some oils oxidize, or 

become acids if they sit too long. Then they 

hydrolyze and react with the base, forming a 

salt that kills the base catalyst before the base 

can react with the methanol used to create 

biodiesel. 

“So what we’re trying to do is create 

a catalyst that instead of being a base is 

actually an acid, which will eliminate the 

free fatty acids before the oils go through the 

conversion process to produce biodiesel,” 

says Lin. “If companies like West Central 

can solve this free fatty acid problem, 

they would be able to really open up their 

markets,” he adds. “For example, there’s a 

10 cent per pound cost difference between 

using poultry fat than using soybean oil to 

create biodiesel.” 

Two-fold process

At the same time Lin is working on the 

free fatty acid problem, one of his colleagues, 

John Verkade, an Ames Laboratory associate 

scientist and an ISU professor of chemistry, 

is working to develop a “superbase” catalyst 

he patented through ISU that would more 

effi ciently conduct the transesterifi cation 

Victor Lin and graduate students Hung-Ting Chen and Jennifer Nieweg line up 

behind samples (left to right) of poultry fat, soybean oil and biodiesel.

Inquiry 2004
17

process, that is converting the triglycerides 

to biodiesel. “So my participation is to 

help John design a system to actually turn 

the homogeneous superbase catalysts into 

heterogeneous systems so these catalysts can 

be recycled,” says Lin. But going beyond 

that, Lin says he has developed a new 

heterogeneous alphacatalyst, containing 

both an acid and a superbase, which would 

eliminate the free fatty acids and also do the 

transesterifi cation. 

“What you’d have is a heterogeneous 

double catalyst,” says Verkade, “one that 

would convert both the FFA and triglyceride 

to biodiesel.” 

Lin adds, “Having one catalyst doing two 

jobs would be like killing two birds with one 

stone.” He notes that this next generation 

super-effi cient catalyst would be useful to 

industry in many ways. “Effi ciency is what 

they’re after, so we would be lowering the 

costs associated with producing biodiesel as 

well as making the catalysts recyclable.” 

As one might imagine, all of this is music 

to the ears of West Central Cooperative. 

“Our interaction with Victor Lin has been 

great,” says Danzer. “They get input from 

us on the practical commercial applications, 

and we get the detailed science.” 

Lin says the cooperative is looking 

beyond just being able to produce biodiesel 

fuel. “It is also considering selling the 

overall production design to potential 

clients,” he says. “Let’s say, for example, 

that California wants to build a biodiesel 

plant. They could come to West Central 

and purchase an entire design package. 

That would be good for them and good 

for us because they would have to buy the 

catalyst from us.” 

West Central has actually taken steps 

to get this process started. It has formed a 

partnership with another Iowa company to 

build what Danzer calls “turnkey” plants for 

other companies. 

Lin believes the Ames Laboratory 

scientists are on the right track to make 

biodiesel a competitive alternative fuel. “I 

think we’re at a crucial juncture that will 

require both know-how and government 

funding,” he says. 

“Tooling up” the biodiesel production 

process will require a major change in 

infrastructure because that infrastructure 

is currently based on fossil fuels, says 

Lin. And changing infrastructure always 

costs money, which he says is where the 

government comes in. “If some changes are 

made, we could see the market for biodiesel 

really open up,” Lin concludes. 

For more information:

Victor Lin, (515) 294-3135

vslin@iastate.edu 

Research funded by:

U.S. Department of Agriculture 

A worker at the West Central Cooperative 

processing plant kneels beside a pair of 

decanters used to separate the lighter 

methyl esters from the heavier glycerine.

Inquiry 2004

Photo courtesy of West Central Cooperative
18

Since their discovery more than 

20 years ago, quasicrystals 

have intrigued scientists with a 

uniqueness and perfection that defi es the 

conventions of regular crystalline materials. 

In a similar fashion, an interdisciplinary 

group of Ames Laboratory researchers is 

drawing on a unique blend of techniques 

and talents to lead the effort to decipher 

how and why these materials form.

First discovered in 1982 at the National 

Institute for Standards and Technology by 

researcher Dan Shechtman, quasicrystals 

are metallic alloys, most of which contain 

60 to 70 atomic percent aluminum. These 

mysterious metallic alloys are somehow 

able to form into crystals – usually with a 

fi ve-fold symmetry – in which the atoms 

are ordered, but without the periodicity 

common in crystalline materials. Though a 

direct correlation to the atomic structure has 

yet to be drawn, quasicrystalline materials 

are hard, slippery, poor conductors of heat, 

and resistant to attack by other chemicals. 

Such properties make them particularly 

useful for applications requiring resistance 

to wear, low adhesion or a thermal barrier.

Scratching the surface

Because such properties relate to 

interactions taking place on the surface 

of the materials, study of the surface of 

quasicrystals was a logical starting point. It 

was also a particularly attractive problem to 

Starfi sh and Farey trees add to the quasicrystal’s allure

by Kerry Gibson

Ames Laboratory materials chemist 

Pat Thiel holds a sea-dwelling starfi sh 

that exhibits the same fi ve-sided 

symmetry as a recently discovered 

phenomenon in which aluminum 

atoms deposited on a quasicrystalline 

substrate cluster around site-specifi c 

holes in the substrate surface in a starshaped pattern.

Deciphering the Quasicrystal

Inquiry 2004
19

materials chemist Pat Thiel, who specializes 

in surface characterization of materials.

“There were some wild speculations 

about the surface of quasicrystals, but when 

we started, those hadn’t been backed up by 

experimental data – no one had really taken 

a look at what was happening on the surface 

of these materials,” says Thiel, who credits 

Ames Laboratory physicist Alan Goldman 

for introducing her to the subject and for 

fostering the Lab’s ongoing research efforts 

in the quasicrystal fi eld.

“It took us a year or so to formulate the 

specifi c questions that needed to be asked,” 

she says, “like what is the structure of the 

clean surface.” According to Thiel, who is 

also an Iowa State University distinguished 

professor of chemistry, even that seemingly 

simple question was controversial. 

Though lacking a periodic structure, 

quasicrystals do contain small clusters of 

atoms. “To create a fl at surface would 

mean cutting through some of the atom 

clusters, and a segment of the research 

community believed that you couldn’t do 

this and have a fl at surface that was also still 

quasicrystalline,” Thiel says, adding that the 

notion was dismissed as heresy by some of 

the more fervent quasicrystal devotees.

Because many quasicrystalline materials 

are aluminum-rich and because aluminum 

oxidizes very easily, it was necessary to 

prepare and study samples in ultrahigh 

vacuum to look at a “clean,” unoxidized 

surface. 

Thiel’s group developed a method 

to clean the surface of quasicrystalline 

aluminum-copper-iron samples with an 

ion beam to remove any surface oxidation, 

followed by heat treatment. Using a 

number of techniques, including lowenergy electron diffraction, her group 

discovered the surfaces are indeed fl at and

quasicrystalline. 

They also found that there are clearly 

layers, as evidenced by stepped “terraces” 

on the cleaned sample. Consistent with 

basic surface science principles, the 

surfaces of these layers were aluminumrich and densely packed, and each layer 

was comprised of two planes of atoms, 0.4 

Angstroms (Å) apart. The visible steps 

were the separation between the favored 

terminations.

Additional study of these layers showed 

that there are recurring features, so-called 

“fl owers” of atom clusters. The fl owers 

were comprised of 20 atoms of aluminum, 

arranged in two rings around one iron 

atom. By connecting the iron centers 

of these fl owers, a clearly pentagonal, 

long-range order emerges in an otherwise 

aperiodic material.

Starfi sh phenomenon

With this new detailed understanding 

of the surface, the next step was to look 

at depositing material back onto a clean 

quasicrystalline surface to see if it would 

act like a template, a phenomenon called 

pseudomorphism. To do this, Thiel turned 

to thin-fi lm techniques that allow layers 

only a few atoms thick to be deposited.

“We know that pure silver, for example, 

doesn’t want to form a quasicrystal in bulk,” 

Thiel says, “but this might be a way of 

forcing it to form a quasicrystal for at least 

one or two atomic layers. Then we could 

see if it had unusual properties due to the 

quasicrystalline structure it was forced to 

adopt.”

Silver and aluminum were chosen 

because they have low surface energies. In 

other words, they easily spread out to “wet” 

the substrate to which they’re applied. To 

deposit these materials, a molecular beam 

source was used to vaporize pure aluminum, 

and the gaseous atoms then landed on the 

clean surface of the substrate.

“These atoms, we believe, are quite 

mobile,” Thiel says. “To our surprise, 

they seem to fi nd very specifi c sites on the 

surface and form in unique arrangements 

that look like starfi sh.”

The “starfi sh” are comprised of fi ve, or 

possibly six, atoms of aluminum that gather 

in a star shape around 2 Å-deep holes in the 

surface of the materials. At this point, it’s 

not clear if a sixth atom locates in the center 

hole.

“This is remarkable for a couple 

of reasons,” Thiel adds. “In a normal 

crystalline material, you have homogeneous 

nucleation where the deposited atoms 

diffuse and collide, and randomly form 

new islands on the substrate. Here, we see 

site-specifi c nucleation – the atoms diffuse 

and cluster at the holes, which are trap sites. 

This scanning tunneling electron 

micrograph of the quasicrystalline 

substrate shows how the atoms of 

aluminum, deposited using thin-fi lm 

technology, gather in star-shaped 

clusters around 2 angstrom-deep holes. 

This site-specifi c nucleation and the 

fact that the “starfi sh” are uniform 

in size represents a breakthrough 

in the understanding of the surface 

characteristics of quasicrystalline 

materials.

Inquiry 2004
20

to fi nd the next one. In the case of the 

rabbits, one pair is produced during each 

of the fi rst and second months. The third 

month, the original pair and the fi rst pair of 

offspring each produce a pair. Three pairs 

are produced the fourth month, then fi ve, 

etc, producing the sequence of numbers 1, 

1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233 

and so on.

In a so-called Farey tree, the “starting” 

numbers are expressed as fractions. Adding 

the numerators and denominators of those 

and subsequent fractions recursively, results 

in a cascading series of values that become 

greater in number but closer in value as 

shown in the diagram on page 21. 

The Zn-Pd system Miller and Gourdon 

are studying seems to follow the same type 

of recursive sequence as the concentrations 

of the two components are varied.

“It gives us a possible recipe,” Miller says 

of the combinations suggested on the Farey 

tree. “We can target certain compositions to 

see if they indeed give rise to an identifi able 

unit cell.”

Miller’s interest in the zinc-palladium 

alloy stems from a phase diagram of the 

material. The diagram shows a region 

of roughly a 70 percent to 80 percent 

concentration of zinc, that indicated a 

metastable “gamma brass” state normally 

associated with quasicrystalline behavior.

At one side of this phase region, a 

sample of Zn11Pd2 exhibited a short linear 

arrangement of zinc and palladium atoms 

that, through the use of X-ray diffraction, 

measured 12.912 Å long. At the other 

side of the phase, a Zn212Pd64 composition 

exhibited a long linear arrangement that 

measured 33.32 Å.

“We wondered if other compositions 

would be expressed as combinations of these 

short and long strings,” Miller says. “So far, 

we’ve been able to show that compositions 

for Zn77.5Pd22.5 and Zn79Pd21 fall as expected

 (according to the Farey tree model) with 

longer and longer clusters comprised of a 

repeating sequence of short and long strings.

“Does this system continue to follow the 

sequence?” Miller asks rhetorically. “We 

don’t know yet. As the unit cells get longer, 

the diffraction points displayed get closer 

and closer together, and given our current 

measuring instrumentation, there comes a 

point where we can’t differentiate between 

individual points anymore.”

According to Miller, the value of this 

and similar research is that it leads to new 

ways of thinking about how materials form, 

especially as they go from liquid to solid 

state.

“One of the beauties of quasicrystral 

research, particularly here at Ames 

Laboratory,” Miller says, “is that it is truly 

interdisciplinary. The study of metals has 

traditionally been the realm of physicists, 

metallurgists and crystallographers, but 

these materials have gotten chemists 

involved, and the molecular viewpoint we 

bring can aid the fi eld in helping interpret 

what’s taking place.”

So the surface is dictating the nucleation, 

and the arrangement of these nanostructure 

islands is not at all random.

“The other interesting thing is that the 

atoms are arranged pseudomorphically,” 

Thiel says. “The aluminum atoms arrange 

in a pentagonal symmetry that they would 

not want to adopt in the bulk. The starfi sh 

are also nearly identical in size, which is 

another level of control not normally seen. 

Nature has manufactured something that’s 

remarkably uniform.”

Following Fibonacci

Starfi sh aren’t the only remarkable 

new phenomenon associated with 

quasicrystals that Ames Lab researchers 

have discovered. While alloys are known 

to exhibit quasicrystallinity in two and 

three dimensions, materials chemists 

Gordon Miller and Olivier Gourdon appear 

to have discovered a one-dimensional 

(linear) quasicrystal in a zinc-palladium 

alloy. Viewed in a single plane, polyatomic 

clusters of zinc and palladium atoms 

form in a repeating motif that appears to 

approach a limiting case described by the 

Fibonacci sequence.

The Fibonacci sequence, named for 

the 13th century mathematician who fi rst 

described it, is one of those mathematical 

puzzles that demonstrates order from what 

initially appear to be random occurrences. 

In his original treatise, Fibonacci used a 

scenario in which a pair of rabbits would 

produce one pair of offspring each month. 

Given that each successive generation would 

take one month before reaching maturity 

and producing yet another pair, Fibonacci 

asked how many rabbits would be produced 

in the course of a year.

The solution can be found by what is 

known as a recursive sequence, in which 

you simply sum the two preceding terms 

Inquiry 2004

“One of the beauties of quasicrystral research, particularly 

here at Ames Laboratory, is that it is truly interdisciplinary. 

 — Gordon Miller
including a 25 cm3

 single crystal of 

icosahedral cadmium-ytterbium (Cd84Yb16). 

Canfi eld specializes in fl ux-growth methods 

for producing rare-earth magnesium-zinc, 

single-grain quasicrystals.

At the other end of the sample sizespectrum, senior scientist Dan Sordelet 

has successfully worked with hot isostatic 

pressing and sintering techniques to develop 

quasicrystalline coatings from gas-atomized 

powders, work that also relies on the MPC 

for the purest materials available.

As a refl ection of this overall strength in 

quasicrystal research, Ames Laboratory will 

host the Ninth International Conference 

on Quasicrystals – ICQ9 – in May 2005. 

Inquiry 2004 21

And Shechtman, the researcher who started 

it all, will be joining the Ames Laboratory 

staff periodically over the next several 

years as a visiting scientist on leave from 

his permanent position at the Technion in 

Israel.

For more information:

Pat Thiel, (515) 294-8985

thiel@ameslab.gov

Gordon Miller, (515) 294-6063

gmiller@iastate.edu

Research funded by:

DOE Offi ce of Basic Energy Sciences, 

 Materials Chemistry Division

This diagram shows how Miller and Gourdon were able to use a Farey tree model 

to predict the unit length of different compositions of compounds in a zincpalladium system. The top two compositions represent the “borders” of the 

quasicrystalline gamma brass phase and represent short and long one-dimensional 

atomic clusters. As the tree cascades down, the subsequent compositions are 

made up of corresponding combinations of short and long clusters.

World-class attraction

One other very key aspect of this 

group approach is the access Thiel, Miller 

and others have to large-scale sample 

quasicrystalline materials to study.

“We’re extremely fortunate to have 

the world’s leading experts in growing 

crystals in Ames Laboratory researchers 

Tom Lograsso and Paul Canfi eld,” Thiel 

says. “And their work is made possible by 

the availability of ultrahigh purity metals 

produced by the Lab’s Materials Preparation 

Center.”

Lograsso, using Bridgeman and other 

crystal-growth techniques, has produced 

a variety of quasicrystalline materials, 
22

Carbon is the sixth most abundant 

element in the universe. It exists 

all around us in nature, and its 

applications vary tremendously with its form 

and properties. We easily associate carbon 

with such items as pencils, diamonds and 

steels, but it’s also found in plastics, paint 

pigments, lubricants, clothes and cosmetics. 

It’s present in many foods, for example, 

asparagus is especially high in carbon. It’s 

found in the sun, stars, and atmospheres of 

most planets. And we know that all living 

organisms contain carbon – there would be 

no life without it. The fact is, the big “C” 

is such a “popular” element that there are 

more than 18 million compounds of carbon 

listed with the Chemical Abstracts Registry, 

a registry system for all completely identifi ed 

chemical compounds.

Now, a group of Ames Laboratory 

physicists have added carbon to a 

superconducting compound, magnesium 

diboride, in a basic research effort to 

enhance the properties of the material. By 

doping MgB2 with carbon atoms, they have 

doubled the magnetic fi eld the material 

can withstand. The work may one day 

ease the expense associated with current 

superconducting materials that generate the 

intense magnetic fi elds required for such 

applications as magnetic resonance imaging 

for medical diagnostics, high-fi eld magnets 

for research, and superconducting magnets 

for particle accelerators. The fundamental 

research on MgB2 is part of an experimental 

effort on superconductivity and correlated 

systems at Ames Laboratory.

MgB2 history

Unlike ordinary conductors, such as 

copper, superconductors conduct electricity 

perfectly, without energy loss due to heat. 

But metallic superconductors, most notably 

triniobium-tin, Nb3Sn, have always been 

hampered by the fact that they must be 

cooled to an extremely low temperature 

before they become superconducting. 

That critical temperature, or Tc, rests near 

absolute zero (0 Kelvin or minus 459 

degrees Fahrenheit), thus cooling has always 

been expensive, requiring large quantities of 

liquid helium.

However, things warmed up in 

2001 when scientists discovered the 

superconducting properties of magnesium 

diboride. They were amazed to see that the 

critical temperature at which MgB2 becomes 

superconducting is 39 K (minus 389 F), 

far warmer than the reigning niobiumtin superconductors, which become 

superconducting at 18 K (minus 427 F). 

The higher Tc of MgB2 also makes cooling 

the material more economical as it allows 

for the use of inexpensive refrigerators in 

place of liquid helium.

Magnesium diboride’s unexpected 

 Researchers fi nd a little dab of 

carbon adds “character”

 to MgB2

Derek Wilke inserts a puck holding a carbon-doped MgB2

wire sample into the quantum-design physical property 

measurement system. The instrument contains a 14 Tesla 

superconducting magnet for performing magnetotransport 

measurements that are used to determine the sample’s upper 

critical magnetic fi eld.

Inquiry 2004

by Saren Johnston

 Up a

Toughening

Superconductor
23

superconducting capabilities generated 

speculation about the material’s potential 

for replacing niobium-tin superconductors 

in various applications, thus reducing the 

expense of those technologies. But for that 

speculation to become a reality, more basic 

research was needed to increase both the 

magnetic field MgB2 can withstand and the 

electric current it can carry. Now, Ames 

Laboratory physicists Paul Canfield, Sergey 

Bud’ko and Doug Finnemore and graduate 

assistant Derek Wilke have done just that.

Perturbed to new heights

Canfield, who is also an Iowa State 

University physics professor, and his group 

were the first to describe the mechanism 

of superconductivity in MgB2. They also 

devised a method of turning boron of a 

given form into MgB2 with a similar form 

by allowing magnesium vapor to diffuse into 

the boron matrix. This patented technique 

has been used to make pellets, wire segments 

and thin films. Their familiarity with MgB2

serves the researchers well in current efforts 

to enhance its superconducting properties. 

“In this game, once you get an idea of 

what the pure material is doing, you want 

to perturb it,” Canfield says. “You want 

to mess with it and see how it responds. 

The problem is that it’s very hard to 

systematically perturb MgB2. It really wants 

to form in a fundamentally pure fashion.”

As it turns out, “messing” with the 

material is one of the things Canfield and his 

group do best. They were able to figure out 

how to get carbon into MgB2. Experiments 

done by Wilke showed that a 5 percent 

substitution of boron with carbon more 

than doubles the magnetic field MgB2 can 

withstand and still remain superconducting, 

raising it from 16 Tesla for the pure material 

to 36 Tesla. Even though the carbon-doping 

of MgB2 lowers its critical temperature to 35 

K (minus 397 F), 4 K less than in the pure 

material, the magnetic field as a function 

of temperature exceeds any of the NbSn 

compounds, which “peak out at around 30 

Tesla,” according to Canfield. “That sounds 

promising, but there are two things still out 

there that need to be resolved,” he cautions.

“One is determining how much current 

you can pass through the material and still 

have it remain superconducting,” Canfield 

continues. “That’s the critical current, and 

it’s still inferior to Nb3Sn.”

Entrapping electrons

Increasing the critical current that 

MgB2 can withstand and still remain 

superconducting is a challenge because 

whenever large electric currents pass through 

a superconductor, tiny whirlpools of 

electrons, called vortices, are created. The 

motion of these vortices saps energy and 

degrades a material’s ability to superconduct. 

Finnemore’s specialty is pinpointing the 

locations of electron vortices, and knowing 

their locations makes it possible to “pin” 

them. 

If electrical and magnetic conditions 

are right, vortices will stick, or pin, 

themselves to nanometer-size precipitates 

in a superconductor. Once pinned to these 

impurities, they no longer move or dissipate 

energy. The trick is to find just the right 

impurity that will trap the vortices yet still 

allow the electricity to flow through the 

material.

“Titanium diboride is our first try as a 

precipitate, and it works without sucking 

out the carbon we added to increase the 

magnetic field,” says Finnemore. He and 

Wilke added the TiB2 using chemical vapor 

deposition, which disperses the element 

uniformly throughout the material. “We 

think it’s just a better way to make samples 

than mixing powders,” Finnemore adds. 

“Over the next few years, we hope to try 

other precipitates using chemical vapor 

deposition.”

Although Canfield is pleased with 

his group’s success in enhancing the 

superconducting properties of MgB2, he’s 

cautious about predicting too much too soon 

in terms of the material replacing Nb3Sn. 

He reminds us that there’s still that “second 

thing” out there that needs to be resolved. 

“Even if we can tweak the critical current 

to be better or comparable to Nb3Sn, there’s 

still the metallurgy of determining how to 

get a sheath around this material and make it 

a useful wire rather than just a lab sample,” 

Canfield says. “That’s just beyond anything 

we do as basic physicists; it will have to 

happen on some engineering time scale. But 

as far as temperature and critical field go, it’s 

now looking better than Nb3Sn on both of 

those parameters. Now, the critical current 

needs to be comparable or better.” 

For more information:

Paul Canfield, (515) 294-6270

canfield@ameslab.gov

Research funded by:

DOE Office of Basic Energy Sciences

 Materials Science and Engineering Division

The image is a cross section of a 5 

percent carbon-doped wire taken with 

polarized light. The picture shows the 

small, ~10-micron-sized grains lit up in 

brilliant colors.

Inquiry 2004
24

Intouch

For Deborah Zorn, the road to Lindau, Germany, and the 54th International Convention of Nobel Laureates began in childhood. The 

Ames Laboratory graduate student from Lincoln, Neb., says she rarely missed an airing of Public Television’s “Newton’s Apple” and 

almost always took summer science classes in Lincoln’s Bright Lights program.

 Zorn is one of 25 top, young researchers from the United States who received full support from the DOE’s Offi ce of Science to attend 

the June 27-July 2 Lindau meeting. There, she interacted with Nobel Laureates and networked with student participants from around the 

world.

“Debbie is interested in all aspects of science and is fearless and successful in attacking problems,” says Mark 

Gordon, Zorn’s major professor and director of Ames Laboratory’s Applied Mathematics and Computational 

Sciences Program. 

Zorn studies theoretical and computational chemistry at Iowa State University. In one DOE research 

project, she is creating and implementing theoretical and computational models to ease the identifi cation of 

properties in new materials being developed for catalytic systems.

Another of Zorn’s DOE projects uses quantum mechanics and molecular mechanics methods to study 

the behavior of certain metals on a silicon surface. The work may lead to atomic wires one atom wide for 

nanotechnology applications.

Zorn credits her father with encouraging her interest in science. “He instilled an interest in science and an 

appreciation for math in me for which I will always be grateful,” she says.

Science is Zorn’s passion, but she’s also an art enthusiast and an accomplished golfer, earning NCAA division III All-American and 

Academic All-American Athlete honors.

“I like to think of myself as a creative person,” says Zorn. “Whether it’s science, art or sports, it’s all about problem-solving. I enjoy 

taking bigger problems and breaking them down until they are similar to something I’ve seen before and that I can solve.”

The director of the Ames 

Laboratory’s Nondestructive 

Evaluation Program, R. Bruce 

Thompson, was one of the scientists 

selected to participate in NEC Extreme 

Science in spring of 2004. This program, 

organized by the NEC Foundation of 

America, brings together middle-school 

students and teachers with America’s most 

accomplished scientists and engineers to 

introduce students to the wonders of science 

and technology. Thompson, who is also 

a distinguished professor of engineering 

at Iowa State University, was selected to 

participate because of his membership in the 

National Academy of Engineering.

Along with Iowa Governor Tom Vilsack 

and Silvia Clark, executive director of 

the NEC Foundation, Thompson visited 

Southeast Polk Junior High School in 

Runnells, Iowa, and Woodrow Wilson 

Middle School in Council Bluffs, Iowa. 

Thompson used real-world examples 

and hands-on demonstrations to give 

the students a glimpse into the world of 

nondestructive evaluation. Covering topics 

such as acoustic waves, why materials fail, 

metal fatigue and accident investigation, 

Thompson showed how the technology is 

applied to detect and prevent failures in 

structures such as bridges, planes and pipes.

According to the Council Bluffs 

Nonpareil Nonpareil newspaper, Woodrow Wilson newspaper, Woodrow Wilson 

8th-grade teacher Ed Stacy said the visit was 

a wonderful opportunity for his students 

to get a fi rm grasp on science. “With this 

opportunity, kids are able to get the fact that 

science is real and is all around them.”

The NEC Foundation of America was 

established in 1991 and endowed at 

$10 million by NEC Corporation and its 

U.S. subsidiaries.

R. Bruce Thompson (right) demonstrates 

nondestructive evaluation techniques to two 

8th-grade students at Southeast Polk Junior 

High. To the students’ left are Iowa Governor 

Tom Vilsack and Sylvia Clark, executive 

director of the NEC Foundation of America.

Science to the Extreme

The Road to Lindau

Inquiry 2004

by Robert Mills

2004

by Saren Johnston
After 14 successful years of stirring fter 14 successful years of stirring 

up enthusiasm for science with 

its annual Regional High School its annual Regional High School 

Science Bowl, Ames Laboratory spiced 

things up even more by adding a middle 

school event to the mix in 2004.

Sixty students, their coaches and parents 

from 10 Iowa and two Minnesota middle 

schools traveled to the Iowa State University 

campus to help launch Ames Laboratory’s 

fi rst Middle School Science Bowl, April 23-

24. The two-day event included building 

and racing hydrogen fuel-cell cars and a 

quiz-bowl-style competition.

Opening comments from Larry Jones, 

an Ames Laboratory associate metallurgist 

who served as science advisor for the Middle 

School Science Bowl, and presentations 

on solar energy and hydrogen fuel cells 

by members of ISU’s solar car club, Team 

PrISUm, prepared students for the much 

anticipated car-construction and car-racing 

activity on the fi rst day of competition.

Why haven’t we always used fuel cells? 

Are all fuel cells the same size? Aren’t solar 

cells expensive? These were just some of the 

many questions Jones and Team PrISUm 

members fi elded from the attentive and 

enthusiastic middle school students. 

Once given the OK, it didn’t take 

long for the students to get their car kits 

opened and the parts laid out on the 

tables. “I think this goes here,” and “No, 

it goes here – let me show you,” were 

comments repeated frequently as the 

students assembled the myriad of wires, 

tubes and other parts to build the cars. Not 

surprisingly, with just a little help from 

Team PrISUm, Jones and other volunteers, 

the students had the hydrogen fuel-cell cars 

assembled in no time at all.

During the construction process, 

volunteers helped the students understand 

how to operate the cars on solar power. 

The students learned how solar power 

can be used to split water molecules to 

create both hydrogen and oxygen gas and 

also how the combining of hydrogen and 

oxygen in a fuel cell can generate electricity 

that can be used to power a car’s motor. 

At the end of the day, the student 

team from Miller Middle School in 

Ames Lab Adds Middle School to the Mix

Marshalltown, Iowa, took top honors in 

the fuel-cell car challenge. “My son said it 

was his best day ever,” said one appreciative 

parent about the fuel-cell car challenge.

The second day of the Middle School 

Science Bowl brought a full day of academic 

competition. At the end of the day, Des 

Moines Central Academy, Des Moines, 

Iowa, won the quiz-bowl part of the 

competition. “Obviously, we were saving all 

of our brain power for today,” chuckled the 

Central coach, referring to her team’s loss in 

the previous day’s fuel-cell car challenge.

The inaugural Middle School Science 

Bowl drew rave reviews from the 

participants. Many of the students made 

a special point of telling competition 

organizers how much they enjoyed the 

two-day event. Said the coach from Ordean 

Middle School in Duluth, Minn., “We’d 

love to come back.”

the Science Bowl 

Fun

Surrounded by members of Team PrISUm, 

Central Academy students prepare their car for 

the start of a race.

by Steve Karsjen

Central Academy of Des Moines, Iowa, took top honors in the 

academic competition portion of Ames Laboratory’s fi rst-ever 

Middle School Science Bowl.

Double Double
Ames Laboratory 

111 Technical and Administrative Services Facility 

Ames, Iowa 50011-3020

(515) 294-9557

http://www.ameslab.gov

Ames Laboratory is a U.S. 

De part ment of Energy lab o ra to ry 

seeking solutions to en er gyre lat ed prob lems through the 

ex plo ra tion of chem i cal, en gi -

neer ing, materials and math e -

mat i cal sciences, and physics. 

Es tab lished in the 1940s with 

the suc cess ful de vel op ment of 

the most ef fi cient process to 

pro duce high-purity uranium 

metal for atom ic energy, Ames 

Lab now pur sues much broader 

pri or i ties than the materials 

re search that has giv en the 

Lab in ter na tion al credibility. 

Responding to issues of national 

concern, Lab sci en tists are ac-

 tive ly in volved in in no va tive 

re search, science ed u ca tion 

pro grams, the de vel op ment of 

ap plied tech nol o gies and the 

quick trans fer of such tech-

 nol o gies to industry. Uniquely 

in te grat ed with in a uni ver si ty 

en vi ron ment, the Lab stim u lates 

cre ative thought and en cour ag es 

sci en tifi c dis cov ery, providing so-

 lu tions to complex problems and 

ed u cat ing to mor row’s sci en tifi c 

talent.

AMES LABORATORY

Inquiry 2004

A U.S. Department of Energy laboratory operated by Iowa State University