INquiry Science and T Science and Technology at the Ames Laborator echnology at the Ames Laborator y 2003y

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

New-generation Catalysts

R&D 100 Winner

Guiding Neuron Growth

Crime Tips from Toolmarks

AMES LABORATORY
2 Hanging Picassos . . . Saren Johnston

 Innovative work is underway to design and prepare a new generation of highly Innovative work is underway to design and prepare a new generation of highly 

 selective and effi cient catalysts that can be tailored to specifi c applications. selective and efficient catalysts that can be tailored to specific applications.

6 Unlocking the Mystery of 

 Amorphous Materials . . . Kerry Gibson

 What happens between the liquid and solid states of metallic glass is a What happens between the liquid and solid states of metallic glass is a 

 mystery that scientists are working to solve. mystery that scientists are working to solve.

 

8 Sunproofi ng Solar Cells . . . Saren Johnston

 Solar cells absorb sunlight effi ciently, but they also degrade substantially in its presence. Solar cells absorb sunlight efficiently, but they also degrade substantially in its presence. 

 Now, scientists are learning how that happens and creating new materials Now, scientists are learning how that happens and creating new materials 

 that are more reliable. that are more reliable. 

 

10 Groovy Plastic Rebuilds Nerves . . . Kerry Gibson

 Nerve cells don’t naturally reconnect, but a thin polymer fi lm developed at

 Ames Laboratory could help “steer” growing nerves so they can rewire themselves. Ames Laboratory could help “steer” growing nerves so they can rewire themselves.

12 Safe and Sound . . . Robert Mills

 Designers of next-generation nuclear power reactors will be able to integrate ultrasound 

 and other nondestructive evaluation technologies into their systems thanks to the work of and other nondestructive evaluation technologies into their systems thanks to the work of 

 Ames Laboratory researchers. Ames Laboratory researchers.

 

14 It's All In the GAMESS . . . Saren Johnston

 The quest to learn more about how things work on the molecular scale has a group of The quest to learn more about how things work on the molecular scale has a group of 

 researchers playing some highly sophisticated and demanding “games.” researchers playing some highly sophisticated and demanding “games.”

16 Shattering Intermetallic Conventions . . . Kerry Gibson

 The discovery of ductile intermetallic materials by a team of The discovery of ductile intermetallic materials by a team of 

 scientists puts these normally brittle materials in a whole new light.

18 The Best Reality Show Around . . . Saren Johnston

 Physicists are working on bridging the gap that separates the quantum Physicists are working on bridging the gap that separates the quantum 

 mechanical world of atomic and subatomic particles and our observable, everyday world. mechanical world of atomic and subatomic particles and our observable, everyday world. 

20 Making their Mark in Forensics . . . Steve Karsjen

 Scientists are developing innovative statistical methods for showing the uniqueness Scientists are developing innovative statistical methods for showing the uniqueness 

 of toolmarks left on tools during the manufacturing process. of toolmarks left on tools during the manufacturing process. 

INtouch 5, 23, 24

 From an R&D 100 Award to a new plasma furnace — catch up on some Ames Laboratory From an R&D 100 Award to a new plasma furnace — catch up on some Ames Laboratory 

 highlights from the past year. highlights from the past year.

Contents

(front cover) This molecular dynamics simulation shows a new mixed-phase solar cell material consisting of clusters (front cover) This molecular dynamics simulation shows a new mixed-phase solar cell material consisting of clusters 

of nanocrystalline silicon embedded in an amorphous matrix. The material is proving more stable in sunlight than of nanocrystalline silicon embedded in an amorphous matrix. The material is proving more stable in sunlight than 

traditional amorphous materials. (see story page 8) traditional amorphous materials. (see story page 8)

(back cover) A well-used lab notebook and cardboard coffee cups converted to pencil holders — sure signs that (back cover) A well-used lab notebook and cardboard coffee cups converted to pencil holders — sure signs that 

a busy graduate student “lives” here. a busy graduate student “lives” here.
from the Di rec tor

Inquiry is published annually by the Ames Laboratory Offi ce 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 research and technology-transfer centers and industrial-outreach programs.

Editor

Steve Karsjen

Managing Editor

Saren Johnston

Art Director

Jan Weedman 

Photographer

Dennis Sailsbury

1 IN

We are indeed pleased to begin this issue of Inquiry by congratulating Marc Porter, Ames Laboratory associate, and his by congratulating Marc Porter, Ames Laboratory associate, and his 

colleague Robert Lipert for winning an R&D 100 Award in 2003. Marc and Bob have been working with a company to colleague Robert Lipert for winning an R&D 100 Award in 2003. Marc and Bob have been working with a company to 

develop the Ramanprobes System for detecting and labeling antibodies, proteins that serve as the body’s natural defense develop the Ramanprobes System for detecting and labeling antibodies, proteins that serve as the body’s natural defense 

system against infectious agents. 

Beyond this R&D 100 recognition, Ames Laboratory scientists continued to perform innovative basic and applied Beyond this R&D 100 recognition, Ames Laboratory scientists continued to perform innovative basic and applied 

research in a variety of key scientifi c areas over the past year. Our cover story features research that may fi nally answer research in a variety of key scientific areas over the past year. Our cover story features research that may finally answer 

a perplexing question that has plagued the 

research community for more than 20 years: 

Why do solar cells degrade in sunlight? 

Research by physicist Rana Biswas and his coworkers is shedding new light on the atomic 

origins of light-induced degradation. It is 

hoped that this work will lead to improved effi ciency and reliability in solar cells.

While Biswas deals with solar cells, Surya 

Mallapragada is concentrating her efforts on 

human cells by spearheading research to regrow nerve cells. Her innovative research uses 

an ultrathin biodegradable polymer to form a 

bridge between severed nerves that provides a 

path for neurons to reconnect. The polymer is 

already showing great promise in tests on the 

sciatic nerves in test animals. 

In other cutting-edge research, Victor Lin is 

involved in innovative work on a new generation of highly selective and effi cient catalysts 

that can be tailored to specifi c classes of chemical reactions. These catalysts may be used in the synthesis of new polymers and fuels. 

Ames Laboratory’s Mark Gordon is leading a group that is expanding a computational chemistry code that provides Ames Laboratory’s Mark Gordon is leading a group that is expanding a computational chemistry code that provides 

extensive and detailed information on how things work on the molecular scale. The software, called GAMESS — General 

Atomic and Molecular Electronic Structure System — may serve as the foundation for the design of new fuels and optical Atomic and Molecular Electronic Structure System — may serve as the foundation for the design of new fuels and optical 

materials and the development of coatings that are resistant to extreme environments. 

In the area of forensics, Laboratory researchers Stan Bajic and David Baldwin are spearheading a project that supports In the area of forensics, Laboratory researchers Stan Bajic and David Baldwin are spearheading a project that supports 

“toolmark” identifi cation as a method for helping connect tools found on suspects to the crimes. The project includes an “toolmark” identification as a method for helping connect tools found on suspects to the crimes. The project includes an 

image database and software tool that ultimately may help the courts put more criminals behind bars.

These are just a few of the fascinating research efforts underway at Ames Laboratory that you can read about in this These are just a few of the fascinating research efforts underway at Ames Laboratory that you can read about in this 

issue of Inquiry. I think you’ll agree our scientists are doing some very exciting things in their efforts to fi nd solutions to . I think you’ll agree our scientists are doing some very exciting things in their efforts to find solutions to 

our nation’s energy problems. 

Copyright 2003 by Ames Lab o ra to ry. Copyright 2003 by Ames Lab o ra to ry. 

All rights reserved. For additional All rights reserved. For additional 

in for ma tion about Ames Laboratory in for ma tion about Ames Laboratory 

or topics covered in this publication, or topics covered in this publication,

please contact:

Editor, Inquiry Inquiry

Ames Laboratory Ames Laboratory

111 TASF

Ames, Iowa 50011-3020 Ames, Iowa 50011-3020

(515) 294-9557

www.ameslab.gov www.ameslab.gov
2003

2 INquiry

Hanging 

“Gatekeeping” strategy promises more active catalysts 

Victor Lin likes to explain his research on improving the effi ciency 

and selectivity of catalysts from an artistic point of view. “Suppose 

you’re walking through a museum and you pass a showroom in 

which the walls are decorated with Picassos,” he says. “You can enter the room if you want — nothing is blocking your way. But if you 

don’t happen to like Picasso, you might see this room and think to 

yourself, ‘Well, I can go in there, but I prefer not to,’ and you pass it 

by. That’s exactly the idea that we use in our gatekeeping strategy to 

prevent various reactants from accessing specifi c catalysts,” says Lin, 

an Ames Laboratory chemist and an Iowa State University assistant 

professor of chemistry.

Material matters

Catalysts are substances that speed up the rates of chemical reactions without getting used up in those reactions themselves. And 

mesoporous inorganic materials are the current craze in scientists’ 

efforts to enhance the catalytic process due to their heterogeneous 

nature. The possibility of incorporating various catalytic functional 

groups into the characteristically large and uniformly arranged porous channels of these materials, allowing control on a nanometer 

scale, makes them ideal candidates for use as catalysts that can be 

easily separated from the products and recycled.

“These mesoporous materials are called nanoporous catalysts because their pore size is typically within one hundred nanometers,” 

explains Lin. The pore diameters are chosen to control the access 

of molecules to the catalytic reaction sites located inside the porous 

cavities of the material. Only the molecules of certain sizes and 

chemical properties are selected and guided to the reaction centers 

where they are effi ciently transformed to the desired products. 

“That creates some very interesting catalytic effects,” says Lin.

Although mesoporous materials with their large surface areas 

are well suited to the task of enhancing catalytic activity, problems 

Hanging 

Victor Lin injects a sample of products synthesized by a gatekeeper-functionalized mesoporous nanocatalyst into a highperformance liquid chromatography apparatus. The yield and purity of the desired product are being analyzed by the HPLC.

 by Saren Johnston
2003 3 INquiry

can arise in terms of selectivity. “Presumably 

reactants can enter the material from all different angles, so this kind of catalyst will not 

provide the kind of selectivity you would like 

to have,” says Lin. “Let’s say you have two 

reactants, A and B, in your starting material 

and both will react with your catalyst. But 

you only want the product from reactant 

A, so you have to find a way to get rid of 

reactant B.” 

According to Lin, it often requires costly 

and time-consuming separation techniques 

to produce a pure starting material containing only reactant A.

Offering a real-world example, Lin notes 

that currently there is a lot of interest in generating biodegradable polymers. “Probably 

the most commonly used polymer these days 

is all petroleum-based,” he says. “Some day 

we’ll use up petroleum — that’s one thing. 

The other thing is that these polymers are 

not biodegradable. So, if you could actually 

create biodegradable polymers with chemical and mechanical properties that mimic 

those of petroleum-based polymers, then you 

could presumably use them to replace petroleum-based polymers. So there is tremendous interest in this area.”

The problem is that petroleum chemistry 

has been around for two centuries so all the 

infrastructures are well established. “You can 

get some cheap starting materials — something really pure and economical to play 

with, whereas in the bio-related world, your 

starting materials are typically a mixture,” 

Lin says. “You have all kinds of different 

things, so separating, or fishing out, the 

right kind of starting materials is usually 

labor-intensive.” 

Nature’s natural roadblock

Separating reactants is often an enormous 

job thanks to a little quirk of Mother Nature 

called chirality in which a three-dimensional 

form, such as a person’s hand, is different 

from its mirror image. Any object that cannot be superimposed on its reflection is said 

to be chiral, and this is the situation that 

exists with certain molecules.

“Chiral molecules look identical, but you 

cannot superimpose them,” says Lin. “They 

have the same number of atoms and the 

same type of composition, but they have 

totally different properties. People have 

been doing chiral separations for years, and 

they’ve been very successful at it, but there 

is no direct connection between that separation world and the catalysis world,” he adds. 

“You don’t have such an integrated package.”

Lin explains that scientists working in the 

area of catalysis must rely on separation science experts to purify the starting materials 

for specific reactions. “Then they hand them 

down to the catalysis people,” he says. “But 

this is not all that feasible anymore because 

the separation costs have become extremely 

high.” 

Incorporating the separation work into 

the catalyst seemed a likely way to bypass 

the time and expense associated with chiral 

separation. So Lin and his co-workers 

began using MCM-41 type of mesoporous 

silica materials, also referred to as Mobil 

Chemical Material 41 silica, to prepare 

nanocatalysts that would include this innovative feature. Making use of the porous 

channels comprising the MCM silica, they 

created a honeycomb-type structure and 

attached catalytic functional groups to 

individual sites on the pore walls and at the 

entrances to the individual channels. 

“The catalytic groups, themselves, have 

absolutely no selectivity whatsoever,” says 

Lin. “They’re just simple and often commercially available catalysts. That’s why 

they’re cheap and easily synthesized. But 

we still want the selectivity,” he reminds us. 

“So what do we do?”

Resolving the selectivity problem involved 

installing chiral selectors, or “gatekeepers,” 

as Lin likes to call them, with the MCM 

mesoporous catalysts. These gatekeepers 

are synthetic compounds or natural products that have a specific chirality, so they 

deter unwanted reactants from reaching the 

catalyst. “If only one reactant is allowed to 

react with the catalyst, you could actually 

accomplish stereochemical control without 

employing very sophisticated and often 

expensive asymmetric catalysts,” says Lin. 

“And you can play a lot of games with this 

kind of strategy.”

This transmission electron microscope 

image shows a cross-section of a mesoporous silica nanosphere. The pores are 

represented by the hexagonally packed 

dots.

More than just pretty piles of powder. The white powder on the upper left is mesoporous silica nanosphere (MSN) material. The light blue and pale yellow powders 

are the MSN functionalized with copper and palladium catalysts, respectively. These 

mesoporous materials can catalyze the syntheses of various conductive polymers and 

structurally align the molecular wire products. The gold and black powders are the 

copper- and palladium-MSN catalysts with their pores filled with two different conductive polymer products.
2003 4 INquiry

Deck the “walls”

Exploring various approaches for designing and fi ne-tuning the degree of functionalization of these single-site mesoporous 

catalysts involves what Lin refers to as 

“decorating the walls.” In a sense, he’s 

hanging his own Picassos, anchoring catalysts to well-defi ned sites at the entrance to 

and on the channel walls of the mesoporous material, creating a “museum room” 

adorned in a way that is inviting to only a 

specifi c reactant. Although other reactants 

could enter, they prefer not to and pass on 

by, much like the museum visitors in Lin’s 

analogy who chose not to enter the room 

decorated with Picassos.

Lin has devised three unique schemes 

for anchoring the groups of catalysts and 

gatekeepers, or chiral promoters, within the 

mesoporous, honeycomb-type structure. 

“The fi rst idea was to decorate the outside of 

the channels with a certain chiral promoting group that allows only one reactant, let’s 

say reactant A, to enter the catalyst, so only 

product A is generated,” he says. 

The second method involves decorating 

the inside of the mesoporous channels by 

placing the chiral promoting groups right 

next to the catalytic functional groups. 

Although the catalysts don’t have any chiral 

promoting abilities themselves, the proximity to the chiral groups may cause them to 

preferentially generate some sort of chiral 

product.

Huge molecules known as macromolecules play a key role in Lin’s third scheme 

for installing gatekeepers. Similar types of 

functional groups, such as acid groups, may 

be attached to each end, or pole, of a macromolecule. “Those chemists who want to 

functionalize an acid group on one side of 

the macromolecule must somehow protect 

the other acid group on the opposite side,” 

says Lin. “So protection and deprotection 

processes will be needed.”

Offering a way to circumvent those processes, Lin says, “In the case of a molecule 

that has one pole hydrophobic and the 

other pole hydrophilic, we could play a 

trick and decorate the interior pore surfaces 

of the catalyst with hydrophobic gatekeepers so that only the hydrophobic pole of 

the molecule would enter the cavity of the 

catalyst. The hydrophilic pole would stay 

outside of the catalyst with the water, and 

the hydrophobic pole would stay inside. In 

that way, we wouldn’t need any protection 

processes,” he adds, noting that this type of 

selectivity would greatly simplify the synthesis of many complex, biologically active 

molecules.

Catalyst collaboration

Lin says the three schemes for designing 

and tuning the highly selective mesoporous 

catalysts will undergo extensive scrutiny. He 

and Marek Pruski, Ames Laboratory physicist and co-principal investigator on the catalysis project, have already obtained several 

key preliminary results that demonstrate the 

feasibility of these new catalytic principles. 

Detailed characterization of these mesoporous catalysts has been provided by solid 

state nuclear magnetic resonance, or NMR, a 

spectroscopic technique that Pruski’s group 

uses and develops. NMR offers unique information about the structure, location and 

dynamic behavior of molecules on mesoporous surfaces, which helps to understand 

how the catalysts work and drives further 

catalyst design.

Theoretical/computational modeling by 

Ames Lab researchers and co-principal 

investigators Mark Gordon and James Evans 

will provide state-of-the-art characterization capabilities for analyzing and predicting structures, molecular dynamics and 

reactivity in these systems. In addition, Lab 

researchers and co-principal investigators 

Robert Angelici, Andreja Bakac, James 

Espenson, and Edward Yeung will perform 

other catalytic studies, including kinetic, 

surface tethering, atom transfer, electron 

transfer and photochemistry, on the reactions that are catalyzed by the new nanocatalysts. 

Controlling the structure and reactivity of 

the MCM mesoporous support material and 

how it interacts with the catalytic and chiral 

sites holds great promise for the design of 

a new generation of highly effi cient and 

selective catalysts. In addition, the research 

efforts of Lin and his co-workers will expand 

the fundamental knowledge about catalysis 

in regard to selectivity, reactivity and kinetics. “We envision that this research will lay 

the foundations for the future development 

of a wide range of novel catalytic systems,” 

says Lin. 

For more information:

Victor Lin, (515) 294-3135

vsylin@iastate.edu

Research funded by:

DOE Offi ce of Basic Energy Sciences,

 Chemical Sciences Division

Iowa State University Biotechnology 

 Offi ce

 

 

Lin’s three methods for anchoring catalysts and 

chiral (or other structural) promoters to the 

pore surfaces of MSN catalysts are: 

Top: Gatekeeper groups allow only reactant 

A to enter the mesopores to yield the desired 

product A.

Middle: Chiral promoting groups are placed 

next to catalytic functional groups inside the 

“decorated” mesopores. The proximity may 

cause the catalysts to preferentially generate a 

product with the desired chirality.

Bottom: In a process called “domain selective catalysis,” the interior pore surfaces of 

the mesoporous catalyst are decorated with 

hydrophobic gatekeepers so that only those 

functional groups on the hydrophobic part of 

the molecule enter the pore and react with the 

catalysts, whereas the same functional groups 

on the hydrophilic side of the molecule cannot 

be converted to products. 

Catalyst groups

Gatekeeper groups

Reactant A

Reactant B

Product A

Achiral catalyst 

 group

Chiral modifer

Achiral Reactant 

Chiral Product 

Hydrophilic Hydrophilic

Catalyst group

Hydrophobic group

Reactant molecule with 

 multiple functional groups

A given functional group
2003 5 INquiry

INtouch

Ramanprobes Wins 2003 

R&D 100 Award

“It’s the assay system du jour,” said Marc Porter. The Ames Laboratory associate and Iowa State University chemistry professor was 

speaking lightheartedly about Ramanprobes, the new-generation 

immunoassay system that he and Robert Lipert, a scientist at ISU’s 

Institute for Physical Research and Technology, developed in association with Christian Schoen, president of Concurrent Analytical in 

Kailua, Hawaii. But the fact is, Ramanprobes is among the elite of 

today’s new technologies, having been selected for a prestigious 2003 

R&D 100 Award.

The R&D 100 Awards, sponsored by R&D Magazine, honor the 

top 100 products of technological signifi cance marketed or licensed 

during the previous calendar year.

Ramanprobes is a highly sensitive labeling and optical detection 

system that can read multiple biomarkers, such as antibodies, concurrently at a single biochip address. Coupled with the selectivity of 

antibody binding, Ramanprobes allows quick detection and identifi cation, and so has great potential for use within the medical arena. 

In emergency applications, it can expedite treatment for such infectious diseases as HIV, hepatitis C, smallpox and botulism. Another 

effort is centered on early cancer detection. Ramanprobes can also 

be used in military applications to detect weapons of mass destruction — all potentially close to single-molecule detection.

Crucial to the success of Ramanprobes is a new line of extrinsic Raman labels developed by Porter and Lipert with signifi cant 

contributions from students in Porter’s research group. Work on the 

optical detection nanotechnology began about fi ve years ago, according to Porter. “In addition to Bob and myself, there have been six 

graduate students and a postdoc working on the project,” he said, 

noting the team has at one time or another included the following 

individuals: Jing Ni, now at BioSpect in South 

San Francisco; Brent Dawson, now at the University of North Carolina-Greensboro; postdoctoral fellow Desiree Grubisha; and graduate 

students Hye-Yong Park, Jeremy Driskell, Betsy Jean Yakes and Jill 

Uhlenkamp. “That’s the gang, so to speak, the people who make it 

all happen,” said Porter.

While Porter and Lipert headed up the work on the extrinsic 

Raman labels and the biochip development for the Ramanprobes 

technology, Schoen led the effort to build the compact, lightweight 

fi ber-optic Raman system, the NanoRaman I Instrument. Together, 

the new labels and the Raman instrument offer a unique optical 

detection technology with signifi cant advantages over state-of-the-art 

fl uorescent systems, including greater sensitivity, enhanced concurrent analysis and instrument simplifi cation.

“The long-range goal is to build a chip that has several different 

addresses, or antibodies, on it,” Porter explained. “The idea, in the

end, is to be able to screen for multiple biomarkers. In early disease 

detection or diagnosis, the sooner you can detect the occurrence of 

a disease state, the greater the likelihood of a successful treatment 

outcome.”

Describing how the biochip is constructed and the placement of 

the extrinsic Raman labels on the chip, Lipert said, “The chips are 

just little gold-coated pieces of glass. On top of the gold substrate, 

we place antibodies for whatever it is we want to detect. The purpose of those antibodies is to selectively capture the antigens from 

the sample.” He explained that the gold-bound antibodies capture 

the antigens as part of a detection scheme known as a sandwich assay. The next step exposes the captured antigens to more antibodies 

that also bind to the captured antigens. 

“The issue is to have some way of signaling that the captured 

antigens are there, and just binding another antibody isn’t enough 

for the sensitivity needed for many emerging applications,” Lipert 

continued. “We need to label that antibody with something we can 

detect at very low levels.” The labeling process involves placing the 

antibodies on gold nanoparticles, 30-80 nanometers in size, which 

are also derivatized with Raman labels. Gold nanoparticles are used 

because when a laser beam is shined on them, they greatly enhance 

the spectroscopic signal from the label molecules.

“In the past, a lot of these kinds of assays were done with fl uorescence labeling,” said Lipert. “Most of these fl uorescence labels give 

very broad spectral features, so there are a limited number of labels 

that you can distinguish concurrently. The advantage of the Raman 

labels is that their spectral features are much narrower, and you can 

think of them more as a fi ngerprint. So you could conceive of an 

assay where you are able to detect many different labels for many 

different antigens simultaneously.”

Porter elaborated, “You’d focus the laser light on one spot, collect 

the light that’s being scattered by the sample, analyze it with the 

monochromator and pick out the different components. So far, 

we’ve detected three different antigens simultaneously, but we think 

we can get up to 30 at one time. We have some ideas on how to do 

it, but now we’re focused on improving sensitivity and reproducibility — learning how to do the measurements on just a couple of 

them really well fi rst before we try to branch out.” 

R&D 100 winners for the Ramanprobes TM

System (left to right): Marc Porter, Iowa 

State University; Christian Schoen, Concurrent Analytical, Inc.; 

and Robert Lipert, Iowa State University.
2003 6 INquiry

Unlocking the Mystery of

 by Kerry Gibson

Here’s a riddle for you. When does a metal 

not act like a metal? 

Give up? When it’s a glass.

Though that question would stump most 

of us — even when we have the answer 

— it’s a no-brainer for Ames Laboratory 

researchers Dan Sordelet and Matt Kramer. 

The real riddle for them is why metals 

take on various glass-like structures and 

properties depending on how the materials 

were processed.

By defi nition, glass — including the 

common window variety — is formed when 

a material is synthesized in such a way that 

a regular crystalline structure isn’t formed. 

This random, or amorphous, arrangement 

of atoms gives metallic “glasses” a number 

of unique physical and sometimes electrical 

and magnetic properties. Compared to their 

crystalline counterparts, metallic glasses 

are more rigid, yet can be formed into 

complex shapes well below their melting 

temperatures. 

Normally, metals have a very regular, or 

periodic, structure in which the atoms align. 

This ordered arrangement contains damage 

mechanisms that allow crystalline metals to 

be permanently bent or dented. The glass 

form of a metal lacks that regular pattern 

to its atomic structure, making it both hard 

and elastic, giving it the ability to snap back 

into its original shape instead of deforming 

— as long as it’s not bent too far. The stress 

it takes to deform the glass this incremental 

amount is much higher compared to many 

typical metal alloys. These fascinating 

materials are diffi cult to study, however, 

because of the ways and speeds with which 

they form. 

“We’re studying materials that have been 

melt-spun — basically a stream of molten 

metal is dropped onto a spinning copper 

wheel and solidifi es in a ribbon before the 

atoms can line up,” Sordelet says. “Another 

way to create a metallic glass is to use 

high-energy mechanical deformation, e.g. 

mechanical milling to basically destroy the 

crystal structure to such an extent that it 

becomes amorphous.

“We’ve also worked with Pal Molian, 

an Iowa State University mechanical 

engineering professor, to use a laser to 

vaporize materials into highly energetic 

atoms and have them condense randomly 

in a thin coating,” Sordelet adds. “But with 

all of these contrasting synthesis methods, 

it’s diffi cult or impossible to fi nd out what’s 

taking place at the atomic level as the 

amorphous structure forms.”

Working backwards

To get an idea of how the atoms are 

arranged in a particular amorphous 

structure, the two researchers work 

backwards, so to speak, through a process 

called devitrifi cation. Basically, it involves 

gradually heating the metallic glass until it 

devitrifi es — loses its amorphous properties 

— and the atoms realign in the metal’s 

regular crystalline pattern. 

Early results show that as they are 

gradually heated, certain metallic 

glasses have an intermediate, metastable 

quasicrystalline phase before returning 

to their normal periodic structures. But 

whether a metastable structure forms, and 

what type of structure occurs, appears 

to depend on how the metallic glass was 

originally created. Sordelet and Kramer 

speculate that how the metallic glass is made 

is closely linked to its original amorphous 

structure.

“Material that was melt-spun forms these 

intermediate quasicrystalline phases clearly 

during devitrifi cation,” Sordelet says, “while 

mechanically milled material does not 

transform into these metastable transition 

states. We’re trying to determine why these 

differences exist.”

Think golf green

Kramer draws an analogy to a golf putting 

green to better illustrate the point.

“You’ve got balls at various points on the 

green,” he says, “and while they all ultimately 

end up in the cup, they take very different 

paths getting there. Some go fairly straight 

in while others follow dips and breaks 

traveling to the hole. The devitrifi cation 

pathway is going be different depending on 

the material’s initial state — where the balls 

start from on the green.

 Amorphous Materials

Dan Sordelet, left, and Matt Kramer stand next to the melt spinner that provides the 

metallic glass samples they’re studying. By devitrifying melt-spun materials, they hope 

to determine how these amorphous materials form in the fi rst place.
2003 7 INquiry

“The balls’ starting positions on the green 

are linked to how they were made,” Kramer 

continues. 

“For example, the ball representing 

the melt-spun metallic glass might have 

several valleys, i.e. metastable structures it 

must roll down into and up out of before 

fi nally reaching the hole. If not hit fi rmly 

enough, the ball could get stuck in one of 

these valleys, which is analogous to the 

amorphous melt-spun ribbon transforming 

into a metastable quasicrystalline structure.”

Because the quasicrystalline phase occurs 

when a metallic glass formed from a liquid 

is heated, but not in a metallic glass created 

by solid-state mechanical deformation, the 

two researchers speculate that even though 

the liquid-formed glass appears to be 

amorphous, its structure isn’t truly random. 

Some unidentifi ed alignment of atoms is 

carried over from the liquid that is similar to 

the symmetry of the initial metastable phase 

that forms. 

In the specifi c case where metastable 

quasicrystals form, many researchers have 

proposed that an icosahedral short-range 

order exists in the liquid prior to quenching 

it into a glass. This local order is retained to 

some degree in the glass, and the similarity 

of its structure with the long-range structure 

of the quasicrystals is energetically favorable 

to form the intermediate quasicrystal 

structure. Upon further heating, this 

intermediate structure ultimately transforms 

into the stable structure for the particular 

metallic alloy.

“From a fundamental viewpoint, we want 

to try to make the linkage between the 

structure that’s in a liquid and the resulting 

amorphous structures that we see,” Kramer 

says, “and identify the relationship of the 

short-range order in the glassy alloy and 

the role it plays in phase selection as the 

materials devitrify.”

Keeping it simple

To help simplify the task, Kramer and 

Sordelet have focused on binary alloys, 

such as zirconium-palladium, because of 

the limited number of ways the materials 

can bond together. Minimizing the possible 

confi gurations also helps Ames Laboratory 

physicist James Morris, who is working on 

developing theoretical models, to explain 

what’s happening.

The interdisciplinary team is also relying 

on some powerful, high-tech tools to 

analyze the materials, such as the Advanced 

Photon Source synchrotron radiation source 

at Argonne National Laboratory. Using 

a novel furnace Kramer helped design 

and build for the Midwest Universities 

Collaborative Access Team at APS, the team 

gradually heats samples of Zr70Pd30 while 

using the high-energy beam line radiation 

to produce X-ray diffraction images of the 

material’s atomic structure. 

“High-energy synchrotron radiation is 

able to probe the entire sample in a time 

span that’s rapid relative to the heating rate 

of the sample,” Kramer says. “That’s critical 

to understand the average behavior of the 

bulk and not just the few microns near the 

surface.”

To take some different “snapshots” of 

the materials, Sordelet and Kramer are 

collaborating with researchers from the 

Centre National de la Recherche Scientifi que 

at the Ecole des Mines in Nancy, France, 

to utilize accelerator facilities in Oxford, 

England, and Grenoble, France, where 

neutrons are used to bombard the samples 

instead of photons. According to Kramer, 

this will complement the X-ray technique 

and provide information on the static 

conditions.

To augment their work with metallic 

glasses, the two researchers are making 

use of a relatively new and unique binary 

quasicrystalline alloy: cadmium-ytterbium. 

This system shows even more promise to 

help unlock the mystery of icosahedral 

short-range order in liquids because it is 

quasicrystalline and melts directly from 

the solid to the liquid without a change in 

composition, a process known as congruent 

melting. This approach should take even 

more variables out of the equation since it’s 

known that the solidifying phase contains 

icosahedral order. 

“We’re fortunate to be able to work with 

Tom Lograsso, an Ames Laboratory senior 

metallurgist,” Sordelet says, “since he’s 

developed methods for working with this 

alloy to produce large-scale, single-grain 

crystals not available anywhere else.”

While the researchers admit they aren’t 

precisely sure where their work will lead 

in gaining new fundamental insight into 

the infi nite range of amorphous structures 

of metallic glasses, there could be some 

practical applications that come out of it. 

Kramer points out that one of the keys to 

forming nanoscale materials is to control 

devitrifi cation.

“When we form something that’s 

amorphous and then heat it up, what 

crystallizes are typically nanocrystalline 

structures 5 nanometers to 25 nanometers 

in size,” Sordelet says, “and that has 

importance in the development of magnetic 

and high-strength materials.” 

For more information:

Dan Sordelet, (515) 294-4713

sordelet@ameslab.gov

Matt Kramer, (515) 294-0276

mjkramer@ameslab.gov

Research funded by:

DOE Offi ce of Basic Energy Sciences,

 Materials Science and Engineering 

 Division

At the heart of the melt spinner is a copper wheel. An induction coil melts the 

material being studied, and a stream of 

liquid metal drops onto the spinning copper wheel. Because copper dissipates heat 

extremely well, the liquid metal solidifi es 

so quickly that it doesn’t have a chance to 

form in its normal, periodic crystal structure and forms as an amorphous metallic 

glass.
When it comes to sunlight, any dermatologist will tell you a little goes a long way. But 

who would have thought the same warning 

would apply to solar cells — the collection 

vessels for energy from the sun.

Solar cells degrade in sunlight — a mysterious fact that has plagued the research 

community for more than 20 years. Discovering how that degradation process takes 

place is essential to the advancement of solar 

cell research and the ability to produce 

lower-cost electricity from sunlight.

Sun damage

“The basic problem is that when you put 

solar cells in sunlight, the effi ciency starts 

to decrease by as much as 15 percent to 20 

percent over a period of several days,” says 

Rana Biwas, a physicist at Ames Laboratory 

and Iowa State University’s MicroelectronRana Biswas may have found the answer to why solar cells degrade in sunlight and has developed computer molecular dynamics 

simulations to describe the three-step process. Pictured on the computer screen and the inset image is the fi rst step in his network 

rebonding process — the breaking of weak silicon bonds in the hydrogenated amorphous silicon solar cell material. In the fi gure on 

the left of the insert, the weak bond (WB) between atoms c-d has broken, creating, in the fi gure on the right, a dangling bond (DB) 

on c and a new bond, d-x, which results in a fl oating bond (FB) at x. 

2003 8 INquiry

ics Research Center. “Obviously, that’s not 

good.” He notes that it’s possible to reverse 

the effect by heating the solar cell material 

in an oven to 170-200 degrees Centigrade 

(338 F_392 F), but adds that’s not possible 

to do in practice.

Solar cells made from hydrogenated 

amorphous silicon, a noncrystalline form of 

silicon, absorb light far more effectively than 

traditional crystalline silicon solar cells. “InSolar Cells by Saren Johnston
stead of a thick, 20-micron crystalline silicon 

fi lm, you can just deal with a very thin, halfmicron amorphous silicon fi lm,” says Biswas. 

“These cells are more cost-effective as they 

involve much less material and processing 

time — driving forces for industry. However, although amorphous silicon absorbs light 

very effi ciently, it suffers from this degradation effect — that’s the bad news.”

Biswas and his co-workers, Ames Lab visiting scientists Bicai Pan and Yiying Ye, have 

been studying the troublesome degradation effect, also known as the StaeblerWronski effect, for the past few years. The 

research includes investigations into the 

atomic origins of the S-W effect and the 

subsequent exploration of possible new solar 

cell materials through computer molecular 

dynamics simulations. The work is part of 

both the Beyond the Horizons project and 

the National Amorphous Silicon Team effort 

within the Thin-Film Partnership Program, 

both cost-shared development programs of 

the Department of Energy’s National Renewable Energy Laboratory. 

A “bonding” experience

Biswas explains that exposure to light can 

cause changes in hydrogenated amorphous 

silicon, resulting in defects known as metastable dangling bonds — bonds that can go 

away only when heated to a high temperature. Dangling bonds are missing a neighbor 

to which they can bond. To remedy the situation, they will “capture” electrons, reducing 

the electricity that light can produce and 

decreasing solar cell effi ciencies. “The question,” Biswas says, “is how does light create 

the dangling bonds?”

With the development of their three-step 

atomistic rebonding model, Biswas, Pan and 

Ye are well on the way to resolving many 

puzzling aspects of the problem. The model 

is based on rearrangements of silicon and 

hydrogen atoms in the hydrogenated amorphous silicon material.

In the fi rst step of the three-step process, sunlight creates excited electrons and 

holes (vacant electron energy states) in the 

material. When the electrons recombine, 

they pair up with holes on the weak silicon 

bonds. The recombination energy causes 

the weak silicon bonds to break, creating 

silicon dangling bond-fl oating bond pairs. 

During the second step, the fl oating bonds 

break away from the dangling bonds and 

move freely throughout the material. This 

occurs when the extra fl oating bond from 

one silicon atom moves to a neighboring 

silicon atom. The third step reveals that the 

short-lived fl oating bonds disappear. Some 

recombine with the silicon dangling bonds, 

which results in no material defects. Others 

“hop” away from the dangling bonds and 

are annihilated when hydrogen atoms in the 

network move into the fl oating bond sites.

Biswas’ three-step rebonding model shows 

that defect creation in hydrogenated amorphous silicon solar cells is initially driven 

by the breaking of weak silicon bonds followed by the rebonding of both silicon and 

hydrogen sites in the material. The research 

represents a signifi cant achievement in 

understanding the atomic origins of the 

light-induced degradation effect in hydrogenated amorphous silicon and so provides 

a vantage point for eliminating this effect in 

the development of new solar cell materials 

— a task on which Biswas is now focusing 

his efforts.

A splendid blend

To improve the effi ciency and reliability of 

solar cells, Biswas and Pan are investigating 

mixed-phase solar cell materials that consist 

of clusters of nanocrystalline silicon embedded in an amorphous matrix. “One of the 

most promising developments has been the 

success of hydrogen-diluted materials grown 

at the edge of crystallinity — the phase 

boundary between microcrystalline and 

amorphous fi lm growth,” says Biswas. “Our 

fi ndings show that the crystallites make the 

mixed-phase materials quite stable, with the 

exception of the grain boundary region. 

 “There’s a great deal of strain at the grain 

boundary because of the mismatch of materials, so we have a lot of excess hydrogen in 

the grain boundary,” he explains. “The role 

of hydrogen is critical because weak silicon 

bonds, dangling bonds and fl oating bonds 

are all removed by hydrogen insertion.”

The mixed-phase materials and solar cells 

made from them have a much greater stability to light-induced degradation than traditional amorphous materials. By developing 

molecular dynamics computer simulations, 

Biswas hopes to learn more about the 

mixed-phase materials at the atomic level 

and discover what aspect or aspects of the 

materials are responsible for the improved 

properties. His research efforts may even 

extend to manipulating the nanoscale structure of the material, allowing the design and 

creation of improved solar cell materials. 

For more information:

Rana Biswas, (515) 294-6987

biswasr@ameslab.gov

Research funded by:

DOE Offi ce of Energy Effi ciency and 

 Renewable Energy, Offi ce of the Solar 

 Energy Technology Program

A new material consisting of clusters of nanocrystalline silicon embedded in an amorphous matrix holds promise for an improved generation of solar cells that are more 

stable in sunlight than today’s technology. 

2003 9 INquiry
Helps Rebuild Nerves by Kerry Gibson

2003 10 INquiry

It takes a powerful microscope to actually 

see what Surya Mallapragada has developed, 

but its impact could be huge, especially 

for millions of people with various forms 

of paralysis. Micrographs showing tiny 

nerve cells growing along in an orderly 

fashion demonstrate how important this 

breakthrough could be in the ability to 

rewire broken nerve circuits in the human 

body.

Mallapragada’s technique uses 

microscale channels cut in an ultrathin 

biodegradable polymer to regrow nerve 

cells. The method has already been 

proven to work for peripheral nerve 

regeneration in laboratory rats, and it may 

one day allow the paralyzed to walk and 

the blind to see.

Bridging the gap

Nerve cells are unlike most other 

biological tissue. When a nerve 

is severed, the part of the neuron 

“downstream” of the injury typically 

dies off. And neurons in the human 

body can be several feet long. Grafting, 

which works well for other tissue such 

as skin, isn’t the best option because 

it’s diffi cult to get the nerve cells to line 

up and reconnect. There’s also a loss of 

nerve function where the donor tissue is 

removed.

“Nerve cells aren’t able to easily bridge “Nerve cells aren’t able to easily bridge 

gaps of more than one centimeter,” gaps of more than one centimeter,” 

says Mallapragada, an Ames Laboratory says Mallapragada, an Ames Laboratory 

associate in Environmental and Protection associate in Environmental and Protection 

Sciences and Materials Chemistry and a Sciences and Materials Chemistry and a 

chemical engineering professor at Iowa chemical engineering professor at Iowa 

State University. “Peripheral nervous State University. “Peripheral nervous 

system, or PNS, axons — the part of the 

nerve cell which carries the impulses — nerve cell which carries the impulses — 

normally have a connective tissue sheath 

of myelin to guide their growth, and of myelin to guide their growth, and 

without that guidance, they aren’t able to without that guidance, they aren’t able to 

grow productively. They tend to branch grow productively. They tend to branch 

out and form in knots.”

Since the nervous system carries Since the nervous system carries 

electrical impulses, it helps to think of 

nerve cells in terms of electrical wiring. nerve cells in terms of electrical wiring. 

Surya Mallapragada has developed methods to put nanoscale grooves on thin polymer fi lms. The grooves help steer nerve cell Surya Mallapragada has developed methods to put nanoscale grooves on thin polymer films. The grooves help steer nerve cell 

growth to allow the “rewiring” of damaged nerves. 

Groovy Plastic
2003 11 INquiry

Bundles of nerves are like an electrical Bundles of nerves are like an electrical 

cable with multiple wires. When a nerve cable with multiple wires. When a nerve 

“cable” is cut and cells die, it would be as 

though the copper wire downstream of though the copper wire downstream of 

the damage disappeared, leaving only the the damage disappeared, leaving only the 

empty plastic insulation tubes. In order empty plastic insulation tubes. In order 

for new copper wiring to push out across for new copper wiring to push out across 

the gap and fi ll in the empty insulation the gap and fill in the empty insulation 

tubes, you’d need a way to guide the wires tubes, you’d need a way to guide the wires 

into the empty insulation. And that’s into the empty insulation. And that’s 

where Mallapragada’s research comes in. where Mallapragada’s research comes in.

Grooves channel growth Grooves channel growth

By working on a cellular scale, she has 

developed a way to help guide neurons so developed a way to help guide neurons so 

they grow in the right direction. Starting they grow in the right direction. Starting 

with biodegradable polymer fi lms only a with biodegradable polymer films only a 

few hundred microns thick (100 microns few hundred microns thick (100 microns 

equals 0.004 inches — signifi cantly equals 0.004 inches — significantly 

less than the thickness of a human 

hair), Mallapragada and her colleagues 

have developed methods for making 

minute patterns on these incredibly thin minute patterns on these incredibly thin 

materials.

“We’ve made grooves three microns to “We’ve made grooves three microns to 

four microns deep to help channel nerve four microns deep to help channel nerve 

cell growth,” Mallapragada says. “The cell growth,” Mallapragada says. “The 

grooves have a protein coating, and we’ve grooves have a protein coating, and we’ve 

also ‘seeded’ them with Schwann cells to 

help promote this growth.” Schwann cells help promote this growth.” Schwann cells 

naturally form the myelin sheath around naturally form the myelin sheath around 

the PNS cells. When guided by this 

sheath, nerves will grow at a rate of three sheath, nerves will grow at a rate of three 

millimeters to four millimeters per day. millimeters to four millimeters per day.

The polymers, primarily poly(lactideco-glycolide) and polyanhydrides, 

degrade when exposed to water, and degrade when exposed to water, and 

Mallapragada has worked to develop 

thin fi lm polymers that bulk degrade 

in layers over a period of time ranging 

from a few days to almost a year. To put 

the microscale grooves in the polymers, 

she has used both laser etching and 

reactive ion etching, relying on the Ames 

Lab’s Environmental and Protection 

Sciences Program and the Microanalytical 

Instrumentation Center’s Carver and Keck 

Laboratories at ISU for the necessary 

equipment and expertise.

After promising in vitro tests, 

Mallapragada worked with biomedical 

scientist Srdija Jeftinija and other 

collaborators at ISU’s College of Veterinary 

Medicine to conduct trials on rats. Small 

segments of the rats’ sciatic nerves, which 

deliver nerve messages to the hind legs, 

were removed and the severed nerves 

“spliced” using a tube or “cuff” containing 

the polymer fi lm. 

A suture at each end holds the cuff 

in place over the nerve ends. Though 

initially unable to move their legs, the 

rats started to regain use of their legs after 

three weeks and were able to function 

normally after six weeks. 

Central nerve challenge

Although the technique has shown 

great promise with PNS cell growth, 

getting similar results with the central 

nervous system, which includes the brain, 

spinal cord and optic nerve, is another 

matter. CNS cells grow differently than 

peripheral nerves, presenting special 

problems. Oligodendrocytes, the 

connective tissue of the CNS, can actually 

inhibit nerve growth. Mallapragada has 

focused the next phase of her research on 

the optic nerve to try to better understand 

how CNS neurons work and grow.

 “There are other factors at work, 

such as chemical and electrical cues,” 

Mallapragada says. “Other researchers 

have had some success injecting 

adult (rat) stem cells into the site of 

the damaged optic nerve. Our hope 

is to eventually develop arrays of 

microelectrodes that will allow us to 

interface the optic nerve with a retinal 

chip ... a bioartifi cial optic nerve, if you 

will.”

The retinal chip, fi rst developed at 

Johns Hopkins University, uses chip 

technology to replace the eye’s rods 

and cones. The technology transfers 

the digital images to the optic nerve 

via electrodes, but is limited by the 

inability to create electrodes that are small 

enough and numerous enough to create 

a resolution suffi cient for the brain to 

decipher the input as it does with normal 

“sight.”

“This research is a strong step forward 

in our basic understanding of nerve cell 

growth and how to engineer materials 

that help the body repair itself,” says Ari 

Patrinos, Director of the Department 

of Energy’s Offi ce of Biological and 

Environmental Research. “We hope the 

groundwork laid by Ames Laboratory will 

soon pave the way for human subjects to 

benefi t from this technology.”

Mallapragada was honored for this 

and related polymer research in 2002 by 

being named one of the world’s top 100 

young innovators by Technology Review, 

a technology magazine published by the 

Massachusetts Institute of Technology. 

She is also associate director of the 

Microanalytical Instrumentation Center at 

Iowa State University. 

For more information:

Surya Mallapragada, (515) 294-7407

suryakm@iastate.edu

Research funded by:

DOE Offi ce of Biological and 

 Environmental Research 

National Science Foundation

Rats similar to this one were used in 

the study on guiding neuron growth, 

in which a section of sciatic nerve was 

removed and the severed nerves spliced 

using the polymer fi lm.

Micrographs of the polymer fi lm show Micrographs of the polymer film show 

the grooved channels (top) and nerve the grooved channels (top) and nerve 

cell growth in the polymer with grooves cell growth in the polymer with grooves 

(lower half) and without (upper).
Nuclear power plants are producing 

electricity at record rates, providing 

about one-fifth of our nation’s electricity. 

Helping to keep them running safely are 

nondestructive evaluation technologies 

developed at Ames Laboratory. By providing 

the ability to peer inside critical pipes and 

structures without having to destroy them, 

NDE has become essential to the nuclear 

power industry.

Now, Norio Nakagawa, a physicist at 

the Ames Laboratory, and his collaborators 

are applying decades of NDE experience 

to future nuclear reactor designs. “We are 

giving NDE consideration while the system 

design is being developed. That’s rather design is being developed. That’s rather 

new in the nuclear business,” Nakagawa 

says. The researchers are about two years 

into the three-year project, part of the U.S. 

Department of Energy’s Nuclear Energy 

Research Initiative.

NERI’s purpose is to address the longterm barriers to expanding the use of 

nuclear power to ensure that the United 

States can meet its future energy and 

environmental needs. The Ames Lab 

portion aims to develop concepts for online health monitoring of nuclear reactors 

to enhance the safety and economy of 

advanced nuclear power plants. In addition 

to Nakagawa, the research team includes 

R. Bruce Thompson and Feyzi Inanc of the 

Ames Laboratory as well as nuclear power 

industry representatives. industry representatives.

The on-line system will provide 

continuous monitoring so that deviations 

from normal operation 

can be detected 

immediately and 

problems can be 

addressed before 

they become serious. 

Moreover, on-line 

monitoring can be 

done remotely, greatly 

reducing exposure 

levels of maintenance 

workers.

Economics are also 

important, of course. 

“For nuclear power to 

be able to compete with 

other methods, it has to 

improve its operational 

costs,” Nakagawa says. 

One way new reactor 

designs achieve this 

goal is by extending 

the refueling cycle to 

four years or more. 

This, however, makes 

today’s “outage-based 

maintenance” approach problematic, where 

critical inspections are done when the 

plant is shut down for refueling, typically 

every 18 months. With the help of on-line 

health monitoring, designers of the next 

generation of nuclear reactors can reach the 

four-year goal to create plants that are safe 

and economically competitive.

Integrated inspections

The Ames Lab team is developing 

concepts that can be engineered into 

advanced nuclear reactor systems. “Our 

integrated inspection approach will help 

these systems achieve their goal of greatly 

enhanced safety and reliability,” Nakagawa 

says. He adds that the team’s concepts are 

generic enough to be used by designers of 

many types of nuclear power systems.

“The key is the on-line, integrated 

monitoring approach,” Nakagawa says. The monitoring approach,” Nakagawa says. The 

fi rst step of the project has been to develop 

the overall concept. “Of course, there 

have been on-line sensors — temperature 

and SOUNDby Robert Mills

Norio Nakagawa is studying the use of eddy current inspection as one of the 

nondestructive evaluation technologies to be built into future nuclear reactors to 

continuously monitor their health.

2003 12 INquiry

Safeand
13

gauges, and so on — but we are expanding 

the scope of the on-line sensor concept to 

the next level,” Nakagawa says.

The second step of the project is to 

identify the most critical areas in need 

of on-line monitoring and then develop 

NDE concepts to address them. The Ames 

Laboratory researchers are also developing 

sensitivity estimates for each technology. 

“That will tell us how much sensor output to 

expect,” Nakagawa says.

The fi rst area is steam generator tubing. 

As the name indicates, a steam generator 

boils the secondary water into steam that 

goes to the turbine. Steam generators 

require a fair amount of tubing to maximize 

heat transfer effi ciency from the core to the 

steam. “The tubing is very important in 

terms of safety inspection,” Nakagawa says. 

One potential problem is magnetite deposits, 

iron oxide that builds up where the coolant 

in a steam tube evaporates. The magnetite 

buildup reduces heat transfer and creates a 

corrosive environment.

To continuously monitor magnetite 

buildup, the Ames Lab team is proposing 

a built-in eddy current sensor. Essentially, 

EC sensors work by using a probe made of 

a wire coil. An alternating current passing 

through the probe generates a magnetic fi eld 

around it. The probe’s changing magnetic 

fi eld generates current fl ow, or eddy 

currents, in the material. In turn, the eddy 

currents produce their own magnetic fi elds 

that generate reaction voltages in the coil. 

The resulting changes in coil impedance can 

be measured to gather information about the 

test material.

EC sensors can be made tough enough 

to survive the elevated temperatures and 

radiation found inside a nuclear reactor. 

For steam generator inspections, Ames Lab 

researchers are proposing a system in which 

an EC coil encircles tubes to provide a way 

to detect potential magnetite deposits inside 

the tube. One coil might even be able to 

monitor several tubes inside of it.

Use the force

Another critical inspection job is 

determining the structural integrity of 

steam generator tubes, especially where 

the tubes are attached to key support 

points, often by welding. For these areas, 

the researchers are studying ultrasonic 

testing using an electromagnetic acoustic 

transducer. Basically, an EMAT generates 

a static magnetic fi eld and an alternating 

electric fi eld inside the test piece placed 

nearby. The resulting Lorentz force acting 

on the test material generates sound waves 

that travel some distance. At the receiving 

end, these sound waves, in combination 

with the magnetic fi eld, produce an 

electrical voltage that can be measured to 

provide information about the test material 

condition.

Unlike the more familiar type of 

ultrasonic testing used in medical 

applications — in which the sensor is 

coupled with the body via a thin layer of 

fl uid or jelly — EMAT ultrasonic testing 

does not require that the sensor and sample 

be in contact. That, and the ability for 

EMATs to withstand high temperatures and 

radiation, makes EMAT UT an ideal NDE 

technology for nuclear power plants.

Moreover, EMAT UT can be used to 

send an acoustic wave, called a guided 

wave, down a tube to inspect its entire 

length. “Hopefully, our studies will tell 

us whether or not we can actually make 

a wave travel as far as needed, about 10 

meters,” says Nakagawa. The researchers 

are also exploring the use of EMAT UT for 

monitoring the reactor pressure vessel for 

cracking.

On-chip detectors

Another area under study is how to better 

monitor radiation levels in the reactor core 

by using radiation detectors, one more proven 

NDE technology. The technology may be 

used to monitor reactor fuel activities and 

perhaps other critical events.

The concept relies on new semiconductorbased radiation sensors. These on-chip 

detectors, about one-fourth the size of a dime, 

can withstand the high temperatures and 

radiation found in a nuclear reactor. 

The researchers are creating models to 

estimate gamma ray radiation intensities as 

functions of locations over the reactor life to 

determine how to best use these detectors. 

For more information:

Norio Nakagawa, (515) 294-9741

nakagawa@iastate.edu

Research funded by:

DOE Nuclear Energy Research Initiative 

program

Ames Laboratory researchers have introduced the concept of on-line sensors to 

monitor the integrity of the next generation of nuclear power systems. These 

concepts, which use nondestructive evaluation methods, are being made available to 

designers of the advanced reactors (one of them is shown here).

2003 INquiry

EC – Eddy Current

EMAT UT – Electromagnetic Acoustic 

 Transducer Ultrasonic Testing

Reactor Core

Monitoring Need NDE Method

Cracking EMAT UT

Reactor Pressure Vessel

Monitoring Need NDE Method

Magnetite Deposits EC, EMAT UT

(Inside Tubes)

Tube/Tube EMAT UT

Steam Generator

Sheet Integrity

Tube Integrity EC, EMAT UT

Monitoring Need NDE Method

Reactor core Gamma Ray

integrity, Radiography

fuel activity

anomalies, and

fuel rod integrity

On-Line Monitoring for Safe Nuclear Power
14

What molecules do and why they do it is 

largely an enigma, a puzzle of giant proportions. But when all is said and done, it’s 

molecular events that, simply put, make up 

the days of our lives. So it’s not surprising 

that scientists continue to search for the 

reasons governing the actions and reactions 

of these mighty bits of matter.

Among those who are looking for answers 

to problems relating to molecules is Mark 

Gordon, Ames Laboratory program director 

of Applied Mathematics and Computational 

Sciences and head of Ames Lab’s Scalable 

Computing Lab. Odds are Gordon may be 

having better luck at the search than others, luck being somewhat of a misnomer as 

it implies a certain degree of chance, and 

Gordon has not left this investigation to the 

game of chance. 

No games, just GAMESS 

Gordon and his Ames Laboratory coworkers are fostering and expanding a 

computational chemistry code that provides 

extensive and detailed information about 

how things work on the molecular scale. 

The General Atomic and Molecular Electronic Structure System, known as GAMESS, 

includes a hierarchy of quantum chemistry 

methods that helps solve problems relating 

to molecules, making possible the design 

of new fuels and optical materials and the 

development of coatings that are resistant to 

extreme environments.

“All of chemistry, which also means all of 

biology, fundamentally involves molecular 

processes — that is, the way molecules react 

or behave,” says Gordon, who is also an 

Iowa State University Distinguished Professor of Chemistry. “Chemistry, biochemistry, 

biology, materials science, physics — all 

ultimately can be reduced to what molecules 

do and why they do it. GAMESS allows you 

to answer those questions.”

Using GAMESS, Gordon, his co-workers 

and the students in his research group are 

making major contributions to the design of 

new rocket fuels for the Air Force. “We’re 

also involved in a Grand Challenge program for the Department of Defense, using 

GAMESS to help design new optical materials, fuels and wear-resistant coatings,” says 

It’s All In the GAMESS

Chemistry code unravels molecular mysteries

2003 INquiry

by Saren Johnston

Mark Gordon (pointing) discusses GAMESS and other projects underway in the 

Scalable Computing Lab with Secretary of Energy Spencer Abraham when the 

Secretary visited Ames Laboratory’s booth at Supercomputing 2002 in Baltimore.

Gordon. “Some of my former students are 

now using GAMESS to study biological 

processes, such as protein behavior.”

Historically speaking

The history of GAMESS goes back to 

1977 when the initial version of the code 

was assembled, under the direction of Dr. 

Michael Dupuis, from several existing quantum chemistry computer programs by the 

staff at the National Resource for Computations in Chemistry. The original project was 

funded by the National Science Foundation 

and the Department of Energy from 1977 

to 1981. However, the continued development of GAMESS from 1982 to present is 

directly due to the funding provided by 

the Air Force Offi ce of Scientifi c Research; 

to the nurturing environment provided by 

Gordon; and to the expertise demonstrated 

by Gordon, Ames Lab associate Michael 

Schmidt and many students and postdoctoral fellows in developing new functionalities and parallelizing the code. Making a 

code operate effi ciently in parallel refers to 

organizing it so that it can take advantage 

of parallel computers — those with several 

processors that can work on different parts 

of a single problem simultaneously. Also, 

contributions to the GAMESS program from 

Gordon’s many colleagues and from students 

who have been in his research group have 

added tremendously to the current robust 

nature of the code.

“GAMESS is what’s called a legacy code,” 

says Gordon. “It existed far before anything 

of its kind, so some features of GAMESS 

have been made parallel from the beginning, 

and some features have been made parallel 

after the fact. I’ve always had at least two 

or three students and postdocs specifi cally 

working on how to make GAMESS more 

parallel,” he says. “It’s our forte — what we 

like to do is develop these very sophisticated 

methods, in many cases with colleagues, 

and make them parallel and more effi cient 

so we can apply them to bigger molecular 

systems. It’s something we do better than 

most.” A major result of this ongoing effort 
15

by the Gordon group is that an increasing 

percentage of the features in GAMESS, especially the most computationally demanding 

ones, can be done in parallel.

Supplementing the software suite

In addition to excelling at writing parallel 

code for GAMESS, Gordon and his Ames 

Lab collaborators, Schmidt and Klaus 

Ruedenberg, who is also an ISU Distinguished Professor of Chemistry, are particularly adept at creating sophisticated and 

complex methods for the software suite that 

address unusual chemical species. 

“When you have chemical reactions going 

on, especially under severe conditions, such 

as high temperature or high pressure, you 

encounter chemical species that you would 

not even call molecules,” Gordon explains. 

“These are things that don’t hang around 

very long, and you may never see them. 

They’re intermediates and may have lifetimes of only picoseconds or femtoseconds, 

but they may be very important in the overall reaction process. One of our goals is to 

develop methods to treat these very unusual 

species, and the more nontraditional the 

method, the harder it is to make parallel.”

An innovative research tool, GAMESS 

includes a novel graphics visualization 

program, MacMolPlt, written for Macintosh 

computers by Ames Lab associate scientist, 

Brett Bode. Gordon says MacMolPlt eases 

the task of interpreting the various complicated calculations performed by GAMESS. 

Ryan Olson, a graduate student in Gordon’s 

group, is developing WinMolPlt, a Windows version of MacMolPlt. “Ryan has half 

a dozen people around the world testing 

this program, so now 

you can visualize the 

results of GAMESS 

calculations if you have a Mac or a PC,” says 

Gordon.

A unique feature of GAMESS is the effective fragment potential, or EFP, which was 

initially developed by Gordon and Jan Jensen, a former graduate student of Gordon’s 

now at the University of Iowa, in collaboration with Dr. Walter Stevens and his group 

at the National Institute of Standards and 

Technology. Stevens is now director of the 

DOE Chemical Sciences Program. Over the 

past decade, several graduate students and 

postdoctoral fellows working with Gordon 

have contributed to the development of the 

EFP method, including current students 

Heather Netzloff and Ivana Adamovic and 

postdoctoral associate Jie Song.

“Sometimes scientists deal with systems 

in which there are so many atoms and 

electrons that quantum mechanics can’t be 

done, even at simple levels,” says Gordon. 

The EFP method is based on quantum 

mechanics, but it’s not quantum mechanics 

— it’s a simple but sophisticated model potential that represents most of the quantum 

mechanics effects at a very reduced computational effort. The EFP method can be 

combined with actual quantum mechanics 

in such a way that a quantum mechanical 

description is required only in that part 

of a chemical system that is undergoing a 

chemical change. The remainder of the 

system is treated with EFPs, so that the 

entire calculation takes orders of magnitude 

less computer time than a fully quantum 

calculation. 

“The EFP is a sophisticated model to predict how solvents effect chemical reactions 

and to predict the behavior of liquids,” says 

Gordon, “and it’s working very well.

GAMESS offers an amalgam of choices for 

quantum mechanical modeling of molecular 

systems. As such, it proves to be an indispensable tool for today’s chemical researchers who have the benefi t and availability of 

increasing computational power to probe the 

molecular world. Evidence of its capabilities is the fact that GAMESS is used at well 

over 5,000 sites worldwide, ranging from 

high schools and research universities in 

the United States and abroad to government 

laboratories and the private sector. And best 

of all, GAMESS is distributed at no cost to 

users by accessing www.msg.ameslab.gov and 

signing a license agreement. 

For more information:

Mark Gordon, (515) 294-0452

gordon@ameslab.gov

Research funded by:

Air Force Offi ce of Scientifi c Research

U.S. Department of Defense

U.S. Department of Energy, Scientifi c 

 Discovery through Advanced Computing

 

 

2003 INquiry

Brett Bode (foreground) and Ryan Olson bring the 

results of complicated GAMESS calculations to life 

through their respective visualization programs, 

MacMolPlt and WinMolPlt.

Members of the Gordon group working 

on GAMESS enhancements are, left to 

right, Heather Netzloff, Jie Song, Ivana 

Adamovic and Michael Schmidt. The 

researchers will make good use of the 

two Sun systems pictured behind them in 

developing new GAMESS techniques.
2003 16 INquiry

Shattering 

 Ames Laboratory researchers identify non-brittle intermetallic compounds

by Kerry Gibson

Scientists have known for more than 

100 years that intermetallic materials 

— compounds consisting of two or 

more metals bonded together — possess 

chemical, physical, electrical, magnetic, 

and mechanical properties that are often 

superior to ordinary metals. The problem 

with these promising materials is that they’re 

quite brittle at room temperature. Until 

now.

 Ames Laboratory researchers have 

discovered a number of rare earth 

intermetallic compounds that are ductile 

at room temperature. The discovery, to be 

announced in an article in an upcoming 

issue of the journal Nature Materials, has the 

potential to make these promising materials 

more useful.

Brittle is the rule

“Many intermetallic materials are too 

brittle to handle,” says Ames Laboratory 

senior metallurgist Karl Gschneidner, Jr. “If 

you drop them, they shatter. But you can 

beat on these new materials with a hammer, 

and they won’t shatter or fracture ... they’re 

that ductile.”

So far, the Ames Laboratory research team 

led by Gschneidner and materials scientist 

Alan Russell has identifi ed 12 fully ordered, 

completely stoichiometric intermetallic 

compounds. In other words, these materials 

are combined in the proper chemical ratios 

and the atoms are properly lined up.

“Intermetallics have been studied for 

decades,” Russell said. “Tens of thousands 

of them have been identifi ed, and there’s 

a whole menu of ‘tricks’ that can be used, 

such as testing them at high temperatures, 

in zero-humidity, or shifting them off 

stoichiometry, to make them somewhat 

ductile. The materials we’re studying 

are the fi rst ones that don’t need these 

contrivances.”

Ames Laboratory senior metallurgist Karl Gschneidner, Jr. demonstrates the ductility of a “button” of yttrium-silver (YAg). 

Unlike most intermetallic materials that are quite brittle at room temperature, Gschneidner and a group of Ames Lab researchers 

have identifi ed more than a dozen rare earth/main group metal (RM) intermetallic compounds that show high levels of ductility 

and toughness.

Intermetallic Conventions
2003 17 INquiry

materials possess much lower unstable 

stacking-fault energies that exist around 

defects in the crystal structure of the 

materials. Because these energies are lower 

in the ductile materials, it may be easier 

for them to plastically deform instead of 

fracturing at the grain boundaries.

“There are particular planes (within the 

B2 structure) that tend to slip most easily,” 

Russell says, “and particular directions on 

those planes where deformation slip occurs 

most easily. However, we have transmission 

electron micrographs that identify slippage 

in a direction we didn’t see in our single 

crystal studies, so there are probably other 

factors at work as well.”

Exceptional understanding

While there may be applications for 

these ductile materials because of their 

other characteristics, such as hightemperature strength or corrosion resistance, 

Gschneidner and Russell hope that studying 

these materials will actually lead to a better 

understanding of the brittle intermetallics. 

“The most exciting thing about them is 

when they break all the rules like this, it 

gives you a great opportunity to fi gure out 

fundamentally why the others are brittle,” 

Russell says. “To see one that’s the exception 

gives you a new perspective on all the 

others.”

Gschneidner adds, “The exceptions 

are the ones you want to concentrate on 

because they can tell you a heck of a lot 

more than all the ones that obey the rules. 

It can steer you in a whole new direction 

and lead to one of those ‘eureka’ moments.”

Since the discovery of these materials 

evolved from work on another project, 

it has received only minimal funding. 

Gschneidner has pursued it as one of his 

interest areas with the other team members 

“volunteering” hundreds of hours of their 

time. In addition to Gschneidner, Russell 

and Morris, the team includes materials 

scientists Alexandra Pecharsky and Josh 

Zhang, senior metallurgist Tom Lograsso, 

nondestructive evaluation researchers David 

Hsu and Chester Lo, visiting physicist Ye 

Yizing, and students David Kesse and Aaron 

Slager. Physicist and Ames Laboratory 

deputy director Bruce Harmon and 

metallurgist Bulent Biner were also involved 

in theoretical discussions of the materials.

Overall, Russell calls the amount 

of knowledge gained per dollar spent 

“absolutely staggering.” However, the group 

has submitted a funding proposal for further 

research to DOE and has fi led a patent 

application for the materials. 

For more information:

Karl Gschneidner, Jr, (515) 294-7931 

cagey@ameslab.gov

Alan Russell, (515) 294-3204 

russell@ameslab.gov

B2 structure key?

By combining a rare-earth element with 

certain main group or transition metals, 

the resulting binary compound has a B2 

crystal structure. That alpha-numeric 

designation, developed by crystallographers, 

means that the compound has a crystal 

structure like that found in cesium-chloride 

(CsCl) in which an atom of one element is 

surrounded by a cubic arrangement of eight 

atoms of the other element. 

The study has focused on yttriumsilver (YAg), yttrium-copper (YCu), 

and dysprosium-copper (DyCu), but a 

preliminary examination of other rare-earth 

compounds showed that cerium-silver 

(CeAg), erbium-silver (ErAg), erbium-gold 

(ErAu), erbium-copper (ErCu), erbiumiridium (ErIr), holmium-copper (HoCu), 

neodymium-silver (NdAg), yttrium-indium 

(YIn), and yttrium-rhodium (YRh) are also 

ductile.

In tensile testing, these materials 

showed remarkable ductility. The YAg 

stretched nearly 25 percent before it 

fractured, compared to 1 percent or less 

for many other intermetallics. In other 

measurements, the materials showed 

fracture toughness values comparable with 

commercial aircraft aluminum alloys.

Why these materials deform while other 

intermetallics shatter isn’t quite clear, 

but theoretical calculations by Ames Lab 

physicist James Morris show that the ductile 

The yttrium-silver button shows dents and deformation from repeated hammer 

blows. The gadolinium-silicon-germanium material was shattered with a light tap 

from the hammer.

Tensil stress-strain properties of 

polycrystalline YAg (solid curve) and 

YCu (short-dash curve) tested in air at 

22 C compared with commercial 3105 

aluminium alloy (long-dash curve).
18

If “all the world’s a stage,” as 

Shakespeare wrote in As You Like It,

then we might logically ask, what’s 

going on behind the scenes? What’s 

directing or orchestrating that daily, 

worldwide grand performance?

A theoretical physicist might 

say this scenario represents a good 

way to think about classical and 

quantum physics. Classical physics 

describes the world we see — the 

stage — with all the players, objects 

and activities we encounter daily. It 

includes everything from the lifesaving Mr. Coffee machine we switch 

on in the morning to the welcoming 

bed we gratefully crawl into at night, 

and all things in between. Classical 

physics is concerned with matter 

and energy on an observable scale.

Quantum physics, on the other 

hand, explains the nature and 

behavior of matter and energy in the 

worlds we can’t see — the atomic 

and subatomic worlds “backstage,” 

if you will. It deals with discrete, 

individual units called “quanta” 

that interact with their entire 

environment and allow a more 

explicit description of the exact 

nature of reality. In the quantum 

mechanical world, it is possible for a 

particle, such as an electron, to be in 

two or more different quantum states 

at the same time. Although the 

atomic world described by quantum 

mechanics is nothing like the world 

we live in, it presides over that world 

— its sets and cast of characters.

Considering the existence of both 

a classical and quantum mechanical 

world, it’s only natural to wonder 

what happens when the two meet. 

At what point does the quantum 

mechanical world end and the 

classical world begin, and how does 

that happen? The issue is one that 

intrigues Ames Laboratory associate 

physicist Viatcheslav Dobrovitski.

The Best 

Searching for the ultimate reality, researchers are investigating the quantum world

“In quantum mechanics, all the 

objects we know are not localized in 

space, but have some spread,” says 

Dobrovitski. “They are cloudy and 

uncertain. So, there is the problem 

of trying to connect the quantum 

mechanical world and our local and 

relatively certain everyday world. 

Many objects that at fi rst sight look 

essentially quantum mechanical, are 

not,” he says. “They can be explained 

in terms of classical statistical 

mechanics. But there are some very 

special states that cannot be explained 

from this point of view. These states 

are quantum mechanical when the 

system is small, but their properties 

make them classical when the system 

becomes suffi ciently large.”

Dobrovitski notes that what he 

and his Ames Laboratory co-workers 

are trying to do is half science and 

half education. “It’s the education 

of ourselves and, hopefully, of other 

people to try to understand which 

states in a system are intrinsically 

quantum and which are, in fact, 

classical. The problem is that all 

true quantum mechanical states are 

strongly entangled.”

It takes two to “tangle”

Quantum particles that have 

interacted with each other can exist 

in pairs in an entangled state — a 

superposition of states that ceases to 

exist when some physical property, 

such as spin, is measured. (Spin is 

the intrinsic angular momentum of 

a nucleus or an elementary particle, 

such as an electron.) Entangled 

quantum particles will retain 

some type of connection, even 

when separated by great distances 

— “spooky action at a distance” 

is how Einstein described it. The 

relationship develops because the 

two particles occupy a joint quantum 

state and move coherently with 

2003 INquiry

Viatcheslav Dobrovitski’s home is a world away in 

Russia. But even at that great distance, it’s more 

accessible than the quantum world that draws the 

young physicist’s attention. To investigate that hazy, 

indistinct world, he uses supercomputers to simulate 

the behavior of quantum states in specifi c environments, a research effort fundamental to the successful 

development and operation of quantum computers.

by Saren Johnston

Reality ShowAround
19

system with choice, Dobrovitski and his 

co-workers are investigating quantum 

oscillations. “Many people believe quantum oscillations are intrinsically quantum,” 

he says, “but in a sense, they are not. They 

belong to this category of classical system 

with choice.”

Dobrovitski has discovered that in some 

cases quantum oscillations can be seen in 

decohered, nearly classical systems — those 

in which nearly all coherence has been 

destroyed between any pair of entangled 

particles. “The remaining quantum part will 

exhibit quantum phenomena. As a whole, 

the system is no longer quantum, but it still 

remembers something of its quantum legacy 

well into the future, until it becomes totally 

classic,” he explains.

“It is a big problem to clearly sort out 

all the phenomena we encounter in the 

transition from quantum to classical with 

choice,” says Dobrovitski. “We have some 

understanding of how it happens, but we 

need to clarify how various systems behave in 

different situations.” 

He adds that the research is intriguing 

from both the basic and applied points of 

view. “On one hand, it’s interesting from the 

aspect of the fundamental understanding of 

the quantum measurement problem,” he says. 

“The other thing is that it might hold some 

interest for quantum computing, because 

this transition from quantum to classical is 

probably the main thing that jeopardizes 

quantum computations.”

Dobrovitski notes that although some 

very small-scale quantum computing has 

already been implemented in quite a few 

systems, the self-destructive nature of 

quantum mechanical states interacting with 

the environment — decoherence — is a huge 

problem. “They decay very fast, so the idea 

is to understand what determines this rate of 

decay and if we can slow it down to where 

more than just a few quantum computational 

steps can be performed,” he says. Such a 

feat would be a signifi cant accomplishment, 

making possible the potential construction of 

modest-size quantum computers that would 

allow certain types of calculations to be 

performed, such as the factorization of large 

numbers. And massive calculations of this 

kind are far beyond the capabilities of any 

classical supercomputer. 

For more information:

Viatcheslav Dobrovitski, (515) 294-8666

slava@axel.ameslab.gov

Research funded by:

DOE Offi ce of Basic Energy Sciences,

 Materials Science and Engineering 

 Division

National Security Agency

 

 

one another. Quantum entanglement is a 

phenomenon that has been demonstrated 

through experiments time and again. It is 

essential to the emerging fi eld of quantum 

computing, allowing individual quantum 

bits, or qubits, to interact with each other 

immediately, yielding enormous gains in 

time and memory for some algorithms.

“Spin City”

“Many quantum states are selfdestructive,” says Dobrovitski. “They decay 

into a mixture of two classical states, with 

the outcome remaining classical in one 

state or the other.” That outcome might be 

triggered by the quantum state interacting 

with an environment of nuclear spins 

that are present in the system. Offering 

a magnetic molecule as an example of a 

classical system, Dobrovitski says it has only 

two possible choices of where to direct its 

spin — wholly up or down. However, when 

the system was quantum mechanical — that 

is, before coherence of different states was 

destroyed — there could be all possible 

superpositions of the spin state. Up, down, 

or any superposition of the two is allowable. 

“In the process of a measurement, the 

system must ‘choose’ the way the spin will 

be directed, and how it chooses this is 

an unsolved problem,” says Dobrovitski. 

“It’s very amazing that a truly quantum 

mechanical system behaving in a quantum 

mechanical way becomes a classical 

system with choice — a system that can be 

described by statistical physics. And now, 

of course, the problem is to understand how 

this choice is made.”

What a state we’re in!

“All right,” said the Cat; and this time it 

vanished quite slowly, beginning with the end 

of the tail, and ending with the grin, which 

remained some time after the rest of it had 

gone.”

 ~ Lewis Carroll

 Alice’s Adventures in Wonderland

Dobrovitski’s research has shown that 

some of the coherences in entangled pairs 

are less stable than others in respect to 

interactions with the environment. “The 

transition from quantum to classical is not 

a simple matter,” he says. “We know now 

that this transition is associated with stealing 

some coherences.”

In their research efforts to add to the 

knowledge base about how a quantum 

mechanical system becomes a classical 

2003 INquiry

a + b

a + b

a + b

U = exp( —iHt)

decoherence

a + b

a + b

U = exp( —iHt)

This fi gure represents the real-life scenario for a quantum computer. The 

coherence of the interacting qubits is 

quickly destroyed, or decohered, by disturbances from the surrounding environment, such as neighboring nuclear spins 

or lattice vibrations. This loss of coherence, or transition from quantum to classical, leads to a rapid generation of errors 

and is the biggest roadblock to quantum 

computations. 

This fi gure represents the ideal, but 

elusive, scenario for a quantum computer. The quantum bits, or qubits, are 

represented by spins that are interacting 

coherently with one another with no 

disruption from the surrounding environment.
2003 20 INquiry

Astronomical — that’s the term DNA 

investigators put on the chances of the DNA 

of one person matching that of another. In 

fact, some estimates place the odds that 

two people will have the same DNA at 200 

billion to one. It’s a certainty level that all 

but assures that when DNA evidence is 

introduced in criminal cases, the criminals 

are likely to land in jail.

What if the statistical certainty the 

courts rely upon when accepting DNA 

evidence was also available at some level for 

matching weapons found on suspects to the 

crimes? Unfortunately, at this time there is 

no scientifi c way of indisputably proving in 

the courts that a tool, such as a screwdriver 

found on a suspect, was the actual tool 

used to perpetrate the crime. However, the 

future might tell a different story thanks 

to two separate, but complementary, 

research projects underway at Ames 

Laboratory. Both projects are attempting to 

help forensics experts make their case by 

examining the uniqueness of toolmarks.

It’s all in the marks

As one might imagine, there are 

many commercial tool-manufacturing 

companies, both in this country and abroad. 

Probably not as well known in the general 

community, but certainly well known in 

the forensics community, is that during the 

manufacturing process and through normal 

use, tools, such as screwdrivers, pliers or 

wire cutters, are left with certain marks, or 

imperfections, embedded on their surfaces. 

These patterns are believed to make each 

tool unique. 

An interesting fact about toolmark 

identifi cation is that when tools are used to 

perpetrate a crime, such as jimmying a door, 

the patterns on the tools are transferred 

to the crime scene. In the past, forensic 

investigators would take a tool found on 

a suspect and visually examine scratches 

made with that tool in the lab to scratches 

on objects from a crime scene. Through this 

visual examination of the toolmarks from 

the tool and on the crime-scene material, 

they would attempt to match the tool to the 

crime. If the scratch patterns matched, the 

Making Their Mark

 

by Steve Karsjen

in Forens ics

Stan Bajic looks at an image of a toolmark embedded in the surface of an ordinary pair of pliers. A forensic comparison microscope is used to capture digital images of toolmarks, which are being entered into a database. Forensic experts can use the database to identify toolmarks produced through different manufacturing processes. 
2003 21 INquiry

investigator had a case. If not, he or she 

didn’t. It all sounds very straightforward. 

And for some time, it was. But recently the 

waters have been muddied in the courts. 

This traditional qualitative approach used 

by forensic investigators, which is based on 

years of experience in forensic examination, 

was recently challenged in a case before the 

Florida Supreme Court (Ramirez vs. State 

of Florida, 2000) and resulted in a critical 

toolmark match being deemed inadmissible 

as evidence. Essentially, the court claimed 

that the “proposition of uniqueness” for 

tools based on toolmarks was a scientifi c 

theory that has been inadequately tested by 

the scientifi c community. 

“In essence, testimony introduced has to 

be proven by scientifi c method,” says Scott 

Chumbley, an Ames Laboratory metallurgist 

and Iowa State University professor of 

materials science and engineering, who is 

working on one of the new methods that 

may help address the Supreme Court’s 

requirements for quantifi cation in toolmark 

identifi cation. Currently, there is no 

concrete evidence out there, nothing in the 

literature to prove tools and their marks 

are unique based on certain manufacturing 

processes, say both Stan Bajic, Ames 

Laboratory associate scientist, and David 

Baldwin, director of the Laboratory’s 

Midwest Forensics Resource Center, coprinciple investigators on the toolmark 

identifi cation project. 

The sum of its parts

Bajic’s research is a two-fold project. The 

fi rst part involves building a database of 

toolmark images. The unique database 

consists of digital images of the striations on 

the surfaces of tools that are produced by six 

different manufacturing processes: fi ling, 

grinding, milling, whetstoning, broaching 

and stamping. 

The Ames Lab database is the fi rst to 

incorporate numerous manufacturing 

methods and so many samples. Past studies 

of these manufacturing processes have been 

done but were limited in the number of 

samples used (less than 10 per study). Bajic 

says building the database will require the 

production of multiple images through the 

use of a forensic comparison microscope 

equipped with a charge-coupled device 

camera. 

To date, the collection of tools being 

imaged for inclusion in the database 

includes screwdrivers, pliers, wire cutters, 

bolt cutters, tin snips, cold chisels, wood 

chisels and pry bars — tools that have 

been acquired directly from commercial 

manufacturing companies. 

In addition, steel blanks have been 

acquired and processed in the Ames 

Laboratory machine shop to produce 

additional, more controlled, toolmark 

samples of the various manufacturing 

processes. Bajic says having both 

commercial and shop-made sample sets will 

provide a large collection of sample sets for 

determining comparison criteria for each 

manufacturing process and yield a statistical 

basis for toolmark comparison.

Originally, Bajic and graduate students 

Amber Umble and Molly Schiel planned 

to take images of 100 sets of tools for 

each of the six manufacturing processes. 

However, each tool presents more than one 

machined surface, so as many as four sets 

of images were collected for each tool. So 

what started out to be 100 images quickly 

turned into 400 images. And after they took 

into account the fact that it was necessary 

to include multiple magnifi cations and 

replicates for each image, the number grew 

to more than 1,000 images per set of tools. 

“Right now we have over 8,000 images and 

by the time this project is done, I imagine 

we’ll have 13,000 images for all these tools,” 

said Bajic.

Once Bajic has all the digital images in the 

database, the second phase of the research 

project will kick in. The images will be 

used to produce a software tool for the 

reduction and analysis of the image data. 

Algorithms will be developed and used for 

the comparison of the various toolmarks. 

Creation of the software is being 

spearheaded by Max Morris, a professor 

in the Iowa State University statistics 

department. Morris, who is also a professor 

of industrial engineering at ISU and an 

Ames Laboratory associate, describes how 

the software will be used in the following 

way. Normally a forensics expert will take 

the samples (one from the crime scene 

and the other from the tool) and put them 

under a microscope. Then the expert will 

move them around and, based on years of 

experience, will try to line them up and fi nd 

a point at which they meld together enough 

to be called a match. 

Morris has actually watched Jim Kreiser, 

Tin snips are just one of the tools whose 

surfaces are being imaged for a toolmark 

database. 

Images (above) show the types of 

toolmarks that can be created during the manufacturing process. The 

fi rst example (top) shows toolmarks 

resulting from broaching; the second, 

broaching followed by laser hardening; and the third, milling.
22 2003 INquiry

a retired toolmark examiner with over 34 

years with the Illinois State Police Forensic 

Science Laboratory system, do this in 

the lab. “We’ve taken notes and asked 

questions and have come back and started 

dealing with how we take the digital images 

provided by the database apart and mimic 

the process the examiner goes through. 

The idea is to do substantially what he 

does with bits of pixels instead of the actual 

image on the microscope,” says Morris. 

And thus far he says the experiment has 

been a success. He and graduate student 

Zhigang Zhou have developed an imageanalysis algorithm that works on a very 

small set of test images. “Basically our 

preliminary results have been perfect,” says 

Morris. “Every time we should get a match 

between two images, it clearly comes up 

with a high degree of similarity. And when 

we shouldn’t get a match, when the images 

are of different items, the index is much, 

much lower.” 

Morris is quick to point out that even 

though the algorithm can mimic the 

behavior of forensic examiners, it will never 

replace what they do because there are 

subtleties in what real toolmark examiners 

do that have taken a lifetime of experience 

and knowledge to develop. 

“We could never build all that into an 

algorithm,” says Morris. “The best we can 

hope for is that the algorithm would be a 

type of fi rst-order approximation for the 

toolmark examiner. We’re hoping to be able 

to do a separation of the obvious stuff very 

quickly so that the toolmark examiner can 

focus his energy on the more complicated 

cases to call,” he adds. 

Ultimately, Bajic hopes the work he 

and Morris are doing will culminate in 

the statistical tools 

necessary for validation 

of the proposition that 

particular manufacturing 

methods produce 

marks on tools that are 

substantially different 

from tool to tool. “In 

the end, what we will be 

trying to say, for example, 

is that the chances of this 

screwdriver having the 

same marks as another 

from the hardware store 

are one in 10,000 or some 

number. That’s what we want this tool to do 

— provide that probability prediction,” says 

Bajic.

Morris admits that there is a lot of interest 

in providing the probability prediction 

Bajic talks about, especially on the part of 

the FBI, which is funding the research. But 

right now he cautions that the software is far 

from being able to do that on a large scale 

because of the variation in the way tools are 

produced by manufacturers. “What we are 

developing is a set of tools that can work 

in the tightly controlled, narrow artifi cial 

population that we’re setting up with this 

database.” he adds. “It’s an important fi rst 

step.” 

Jumping a dimension

Stepping from a two-dimensional to 

three-dimensional look at toolmarks is 

the goal of Chumbley’s research. He and 

co-principal investigator Larry Genalo are 

using 3-D characterization methods and 

statistical methods to identify toolmarks. 

Their research involves using a profi lometer, 

a scanning tool that measures the height or 

depth of toolmarks and then develops a type 

of contour map of the marks from the scan. 

This map can then be used to precisely 

identify a toolmark, allowing forensic 

specialists to match the mark on the tool to 

the tool manufacturer. 

Like Bajic’s work, this scientifi cally tested 

technique may also one day address the 

needs of the court system for providing 

quantifi able scientifi c data with known 

measures of reliability. Preliminary results 

show the reproducibility of the instrument is 

better than 99.9 percent on known samples. 

“It’s a pretty good fi t,” announced 

Chumbley during a presentation at the 

Midwest Forensic Resource Center’s annual 

meeting in June at Ames Laboratory. The 

MFRC consists of crime laboratory offi cials 

from across the Midwest, and Chumbley’s 

research project is one of fi ve projects 

currently being funded by the MFRC at the 

Ames Lab and Iowa State. One of those 

attending the MFRC meeting was Mike 

Stone, a member of the Omaha Police 

Department’s crime laboratory, who perhaps 

best summarized the criticality of all of 

the toolmark research underway at the 

Ames Laboratory. Reacting to Chumbley’s 

presentation, Stone said, “This research has 

great application to my world. Everything 

we do is geared toward the discovery and 

identifi cation of evidence.” 

For more information:

Stan Bajic, (515) 294-2086

sjbajic@ameslab.gov

David Baldwin, (515) 294-2069

dbaldwin@ameslab.gov

Scott Chumbley, (515) 294-7903

chumbley@iastate.edu

Research funded by:

Federal Bureau of Investigation (work by 

 Bajic and Baldwin)

National Institute of Justice through the

 Midwest Forensics Resource Center

 (work by Chumbley and Genalo)

A digital image of the tip of a screwdriver 

dramatically demonstrates the uniqueness of toolmarks created during grinding, one of the many manufacturing 

processes used to produce tools.

This image of an American Eagle on a 

Sacagawea dollar resulted from a scan by 

a profi lometer. The scan is used to create 

a contour map that illustrates the detail 

and resolution that can be produced by 

the instrument.
23 2003 INquiry

INtouch

New Furnace a Real “Hot Shot”

Ames Laboratory’s Materials Preparation Center has a new, 

powerful tool in its arsenal that even the toughest alloys can’t 

withstand. Capable of generating temperatures in excess of 10,000 

degrees Celsius, the Retech Model 150 Plasma Lab Furnace will melt 

about anything.

 “There’s no limit to the metals or metal alloys it can melt,” says 

MPC director Larry Jones. “We are using it primarily for melting 

reactive metal alloys, but it gives us enhanced capabilities in other 

areas as well.”

 One of the advantages of the furnace is that reactive metal alloys 

can be melted without the need for a crucible. “Some materials can’t 

be melted in a typical crucible furnace because they react with the 

crucible material, contaminating the molten metal,” Jones says. “This 

new furnace doesn’t require such crucibles, so we eliminate that 

problem. 

Instead, the metal alloy is hydraulically pushed into the chamber 

by a bar feeder. The plasma torch moves back and forth across the 

end of the bars as they stick out over a water-cooled, thick copper 

mold.”

 Even though copper has a lower melting temperature than many 

metals, it is used for molds because it conducts heat so well. Heat 

is transferred so quickly to the cooling water that the molten metal 

cools, solidifi es and shrinks away from the surface of the copper 

before the copper melts. The mold forms the melted material into 

an ingot. 

The heart of the furnace is a plasma torch that uses a helium 

and argon mixture as the feed gas. The plasma torch works by 

injecting the feed gas into a hollow electrode. The gas then carries 

an electrical arc from the electrode through a nozzle and to the 

grounded workpiece. The electrical discharges add energy to the 

gases in order to increase the gas temperature beyond that normally 

attainable by chemical reaction.

 One of the initial tasks for the furnace has been to consolidate 

material, turning multiple pieces of long metal bar stock or piles of 

granular material into short, stout ingots. This dramatically reduces 

the overall surface area and lessens the amount of surface oxidation 

that takes place while the metals are being stored for future use.

 “Beyond that, we can do any number of things when it comes to 

melting and reforming materials,” Jones says, “and it’s just one more 

capability we have to meet the research needs of our scientists.” 

“A nation that embraces basic research embraces a brighter 

future,” said Secretary of Energy Spencer Abraham speaking 

at the all-hands meeting of employees during his 2002 visit to 

Ames Laboratory. The Secretary had come to the Lab to formally 

recognize and open the Midwest Forensics Resource Center, a 

facility that serves the needs of regional crime labs and expands the 

capabilities of forensic science. 

Time and again throughout the all-hands meeting Secretary 

Abraham emphasized the importance and value of basic research 

to the Department of Energy’s mission of ensuring national security. 

“In my view, a serious commitment to national security demands a 

serious commitment to science, including basic research,” he said. 

“This commitment strengthens our energy security, international 

competitiveness, economic growth and intellectual leadership.”

Congressman Tom Latham accompanied the Secretary on his 

visit to Ames Lab. Latham was able to secure $3 million in funding 

to help establish the MFRC, which is directed by David Baldwin, 

who also directs the Lab’s Environmental and Protection Sciences 

Program.

During the Secretary’s brief visit, he met with three of the Lab’s 

R&D 100 Award-winning scientists: Ed Yeung, John McClelland 

and Iver Anderson. Each scientist introduced the Secretary to his 

individual research efforts, two relating to forensics investigations 

and homeland security and another highlighting metallurgical 

techniques that contribute to the Lab’s continuing status as one of 

the world’s premier materials science labs.

Concluding his remarks at the all-hands meeting, Secretary 

Abraham said, “I’m very proud to be the Secretary of Energy and 

have the chance to work with people like yourselves. At the end of 

the day, it’s only the men and women in the front lines who make 

the breakthroughs, who bring their talent, curiosity and skill to 

translate that research work into remarkable achievements like 

those that have been undertaken here.” 

A Visit from the Secretary

Secretary of Energy Spencer Abraham (left center) and U.S. Rep. 

Tom Latham (right center) join Ames Laboratory Director Tom 

Barton (far right) and Iowa State University President Gregory 

Geoffroy (far left) prior to the Secretary’s all-hands meeting with 

Lab employees.

Research technician Arne Swanson holds an ingot of material 

that was consolidated in the bright blue Retech 150 plasma furnace, shown behind him in the Materials Preparation Center.
24 2003 INquiry

industry,” Barton said. “These ties are essential if we are to help 

build Iowa’s and our nation’s economy.”

The FLC is a nationwide network of more than 700 federal 

laboratories and centers and their parent departments and agencies. 

The FLC’s primary focus is moving federal laboratory research and 

technology into the mainstream of the U.S. economy. Each year, 

the FLC’s awards committee receives nominations for director 

of the year from FLC members. The selection is made based on 

each nominee’s ability to enhance technology transfer in economic 

development or apply research to technological advancements in 

the fi eld.

“Because of the competitiveness and prestige of the award, being 

selected as a recipient is an honor which recognizes both the 

excellence of your efforts and your facility’s technology transfer 

program,” said Ann Rydalch, chair of the FLC, in a congratulatory 

message to Barton. 

Barton has been director of the Ames Laboratory since 1988. 

The Laboratory’s technology transfer program provides numerous 

opportunities for companies to collaborate with the Lab, from 

contract research to licensing of intellectual property. 

“It makes you feel good to help a company,” Barton added. “After 

all, they’re paying for it. Their tax dollars pay for our work.” Since 

1986, 136 U.S. patents have been issued on technologies resulting 

from Ames Laboratory research. In addition, Laboratory research 

has been the basis for 14 start-up companies. The most recent 

of these is CombiSep Inc., which manufactures the MCE2000, a 

sophisticated instrument for separating and measuring a variety of 

chemical compounds. 

This is not the first time Barton has been recognized by the 

FLC. In 1999, he was elected a member of the organization’s 

National Advisors Group. This select panel of approximately 15 

people provides guidance to the FLC in pursuing its technologytransfer goals and making the organization more effective. The 

group includes senior agency officials, laboratory administrators 

and industry leaders. As part of his award, Barton participated in 

the annual FLC Laboratory Directors’ interactive forum, “Directing 

the Future,” which took place the morning following the awards 

ceremony. 

Since 1999, the Federal Laboratory 

Consortium has been honoring 

outstanding Laboratory directors with its 

Laboratory Director of the Year award. 

One of this year’s recipients is Tom Barton, 

director of the Ames Laboratory. 

The Laboratory Director of the Year 

award is given annually to directors who 

have made outstanding contributions 

supporting technology transfer activities at 

their laboratory. Barton received the award 

on May 7, 2003, at the FLC National 

Meeting in Tucson, Ariz. 

“It’s an honor to be recognized by the FLC because this 

organization represents the best in efforts to help federal 

laboratories, such as Ames Laboratory, strengthen ties with 

INtouch

Iowa State University President Greg Geoffroy 

congratulated Tom Barton in a letter of recognition:

“Congratulations on the very good news that the Federal Laboratory 

Consortium for Technology Transfer has named you Laboratory Director of the 

Year. You have worked tirelessly in shaping the focus of the Ames Laboratory 

and making sure that the Ames Lab is accessible to industry. Your efforts have 

succeeded in making the Lab a rich resource for Iowa business and industry, 

and you have helped, therefore, to generate needed economic growth for the 

state.”

Ric Trotta (left), Chair of the FLC Advisory Council, presents a 

plaque to Tom Barton recognizing him as a Federal Laboratory 

Consortium Laboratory Director of the Year.

Barton Named FLC Laboratory Director of the Year
Annual competition has huge following

None of us is too thrilled about giving up a Saturday for something that’s not essential 

to our usually packed weekend agenda. But Science Bowl, well, that’s another matter!

Annually, on the last Saturday in January, approximately 48 high school teams and 75 

Ames Laboratory and Iowa State University volunteers take over every available room in 

Iowa State’s Memorial Union to participate in the daylong science competition. Happily, no 

one seems to mind losing a little extra sleep on a Saturday morning, putting off household 

tasks, postponing study plans, or even missing Saturday morning cartoons to take 

part in the exhilarating event. And this year was no exception.

Forty-four Iowa high school teams showed up for the Jan. 25th competition. But it was 

Cedar Rapids Washington High School in Cedar Rapids, Iowa, that came from behind in 

the closing seconds of the championship match to win the 2003 Ames Laboratory/Iowa 

State University Regional High School Science Bowl. Washington won all 10 of its matches 

to advance to the U.S. Department of Energy’s National Science Bowl, May 1-5, in Washington, D.C. 

Many of the schools participate in Science Bowl year after year. “It’s our favorite competition of the year,” said Phyllis Bishop, Science Bowl coach from Chariton High School. “It’s 

always so well planned and run in a very effi cient manner.”

Coach Rhonda Thompson of Decorah High School said, “Thank you for the Science Bowl 

experience. My team of rookies really enjoyed it, felt proud to have done O.K. against 

mostly older teams, and are already looking forward to next year.”

Volunteers, too, fi nd they enjoy the Science Bowl experience and the opportunity to 

interact with so many smart and gifted students. “Working with youth and promoting 

science education is one way I can ‘pay back’ for support I received,” said Donald Lewis, an 

ISU entomology professor and a longtime Science Bowl volunteer. “Reading questions at 

Science Bowl helps keep me humble. These students are so bright and talented, and they 

know so much about so many different things. I am awed by their abilities and reminded 

of my own limitations.”

L ve That Science Bowl!

The Ames Laboratory/ISU Science Bowl winning team from Cedar Rapids Washington High School, left to right: Jeff Barnes, Ashley Noreuil, Jake Thomas, 

Krystal Garringer and Aaron McDowell.

“I can’t believe I did that!” Perhaps Joe Hove, 

captain of the Solon High School team, forgot 

to wait until the moderator recognized him 

before giving his answer — a definite Science 

Bowl “no-no” as the question is then offered to 

the opposing team.

Surprise, relief, exhilaration — Cedar 

Rapids Washington coach Heather Adams 

displays some of each emotion as her 

team wins the 2003 Ames Laboratory/ISU 

Science Bowl.

Although many of the people who 

volunteer for Science Bowl have scientifi c 

backgrounds, just as many don’t. “There 

are tasks available for everyone, such as 

timekeeping and scorekeeping,” said Ellen 

Price, an Ames Lab account specialist who 

just completed her third year as a timekeeper for the competition. “Since you 

don’t have to be a scientist or need special 

skills to help, it’s something I can do and it’s 

also an opportunity to represent Ames Lab 

in a positive way. It’s a fun and energetic atmosphere, and it’s interesting to hear part of 

the competition and see all the high school 

teams that come to participate.”
Ames Laboratory 

111 Technical and Administrative Services Facility 

Ames, Iowa 50011-3020

(515) 294-9557

http://www.ameslab.gov

INquiry

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