Duke Research Blog

Following the people and events that make up the research community at Duke.

Author: Ashley Yeager (Page 2 of 11)

Students Create Multimedia Ocean Conservation Text

By Ashley Yeager

This screenshot shows one of the opening page of of Johnston's new iBook. Image courtesy of Dave Johnston, Duke.

This screenshot shows one of the opening pages of a chapter in Johnston’s new iBook. Image courtesy of Dave Johnston, Duke.

Duke marine biologist Dave Johnston and his students are back in business on iTunes.

They’ve just released The View From Below, a free iBook for middle school students and teachers that uses multimedia and classroom exercises to discuss overfishing, marine debris, climate change, invasive species and other issues related to marine conservation.

This is Johnston’s second digital textbook. His first was Cachalot, an iPad textbook covering the latest science of marine mammals like whales, dolphins and seals. Experts contributed the text, images and open-access papers.

The View From Below, however, is a bit different.

Undergraduate students in Johnston’s Marine Conservation Service Learning class wrote the book using Apple’s iBooks authoring tool. Johnston and Tom Schultz, Director of the Marine Conservation Molecular Facility at Duke’s Marine Lab, edited it.

“There are a lot of people exploring the use of the iBooks platform for student-generated content, among other development platforms,” Johnston says. “I don’t think we’ve seen many that focus on marine science yet though, and I’m pretty sure it’s the first marine conservation textbook written by students on the iTunes store.”

Johnston says the class chose to use the iBooks software because the technology is free, easy to use and provides “great templates to get things going quickly.” The software also works well because Duke’s Marine Lab has an iPad loaner program, making the tablet the platform of choice for developing and testing the textbook.

The middle school that the service learning class works with also has access to iPads for students and instructors, so the audience was there for the iPad format, Johnston adds.

His students chose to write the book as the class project to spur learning and discussion about some of the most serious problems facing Earth’s oceans.

“As the text indicates, all life on earth is ultimately supported by the ocean, so we need to take care of it,” he says.

Chocolate’s crisp crack comes from chemistry

By Ashley Yeager

This is the final post in a four-part, monthly series that gives readers recipes to try in their kitchens and learn a little chemistry and physics along the way. Read the first post here and the second one here and the third one here.


This bunny must have been made from quality chocolate. His ears are already gone. Credit: Waponi, Flickr.

When you snap off and savor the ears of a chocolate bunny this Sunday, say a quick thanks to science.

“The essence of science is to make good chocolate,” said Patrick Charbonneau, a professor of chemistry and physics at Duke.

He explained that cocoa butter, one of the main ingredients in chocolate, can harden into six different types of crystals. All six types are made of the same molecules. But, at the microscopic level, the types have distinct molecular arrangements, which lead to differences in the crystals that form.

“The problem with chocolate is that only two of these types have good texture when eaten,” Charbonneau told students in the Chemistry and Physics of Cooking.

He teaches the freshman seminar with chef Justine de Valicourt and chemistry graduate students Mary Jane Simpson and Keely Glass.

During class, students looked at and tasted chocolate containing only the good-tasting crystal types and some that also contained the less favorable ones. The first had that signature sheen and snap of quality chocolate and melted evenly when left on the tongue. The latter pieces were dull, melted with the slightest touch and left a sandy texture on the tongue.

The demonstration showed that the different types of chocolate crystals melt at different temperatures. By carefully controlling the chocolate as it cools, chocolate-makers can create mixtures of only the favorable crystal types.

The process, called tempering, takes chocolate through a series of heating and cooling steps. The initial cooling step forms many of the chocolate crystal types, including the dull, unfavorable ones. Warming the mixture a little — to about 31°C (87°F) — melts the unfavorable crystals but not the best-tasting ones.

As the mixture cools again, the remaining, favorable crystals “seed” the chocolate so that good-tasting crystals form preferentially throughout, ensuring good chocolate structure and taste.

Students got a chance to test the science in lab later that evening, and judging by the number of mouths (and faces) covered with chocolate, it’s safe to say the science was successful.

If you’re looking to try it out — or save a poor bunny’s ears — here’s the recipe.

Tempering chocolate:

1 small, microwave safe bowl
1 big bowl
1 spatula
2 scraper spatulas
1 chocolate mold
parchment paper
cooking thermometer

250 g Dark Chocolate or 250 g Milk Chocolate (about 1 1/3 cups)

60g white chocolate (about 1/4 cup)
60g yogurt (a little less than 1/4 cup)


1. Place milk or dark chocolate in the small bowl.
2. Heat the bowl in 30-second intervals in a microwave (stirring after each) until the chocolate is melted. Note: The milk chocolate should take about 1.5 minutes and the dark chocolate about 2 minutes to melt.
3. Once heated, pour half the liquid chocolate onto a clean marble or stone counter. The chocolate puddle should be the size of a medium pancake. (Note: If there is not stone or marble surface, another technique is to melt less chocolate and then add good tempered chocolate in it to lower the temperature.)
4. Spread the pancake portion out in ribbons using the scraper spatula. Bring the chocolate back together into a mound repeatedly for 5 minutes, until it starts to solidify.
5. Put the chocolate back in the original heating bowl. Adding the cooler chocolate will cool the rest of the liquid to the right temperature.
6. Mix the cold and hot chocolate.
7. Check the temperature of the chocolate. (Dark: 31-32°C/88-89.5°F; Milk: 29-30°C/84-86°F).
8. Dip the parchment paper in the mixture of the “hot” and “cold” chocolate. If it cools on the parchment paper and is uniform and shiny, then it’s ready.
9. Pour chocolate into mold.
10. To make stuffed chocolate candies, flip the mold to empty excess chocolate.
11. Turn it back, scrap the excess of chocolate off the surface. Let the thin layer of chocolate in the mold crystallize.
11. Melt white chocolate. Mix it with yogurt. Cool to room temperature.
12. Add filling to 2/3 of the mold cavities, and then pour more tempered chocolate on top.
13. Level the chocolate with a scraper and scrape off excess.
14. Let it rest for few minutes at 20°C (68°F) or put it in the fridge.
15. Pop candies from mold and enjoy.

Duke Math Makes Final Four

By Ashley Yeager

This NCAA bracket is based on the quality of the school's math department. Courtesy of: Jordan Ellenberg, UW-Madison.

A few mathematicians made their NCAA bracket based on the quality of universities’ math departments. Courtesy of: Jordan Ellenberg, UW-Madison.

If NCAA basketball championships were won with math, Duke would move on to the Final Four.

At least, that’s what Jordan Ellenberg, a University of Wisconsin mathematician, and his friends think.

They didn’t use complex algorithms to make their bracket, but picked their winners based on the quality of each school’s math department.

With that ranking scheme, Harvard would win it all, with Cal second and UCLA and Duke rounding out the Final Four.

“Of course, these judgments are for entertainment only, and were produced by a group, so if you find any of the picks absurdly wrong, those were the ones I didn’t make,” Ellenberg wrote on his blog, where he posted the picks.

Sadly, the bracket isn’t doing so well as March Madness moves forward.

But it is a fun way to learn more about the math departments around the country and how well their quality does, or does not, correlate with the quality of the schools’ basketball teams.

Special thanks to Duke mathematician Jonathan Mattingly for pointing the bracket out to us.

Go Duke!

Local high-schoolers analyze real LHC data at Duke

By Ashley Yeager

Duke physicist Mark Kruse explains a few finer points of analyzing LHC data to two NCSSM students. Credit: Ashley Yeager, Duke.

Duke physicist Mark Kruse explains finer points of analyzing LHC data to two NCSSM students. Credit: Ashley Yeager, Duke.

Thin, blue lines spider across the computer screen. With a click on one, a solid blue peak on a bar graph pops up. A click on the other line makes a similar graph. Looking at them closely, two high-schoolers decide if they could be signatures of a particle called a Z-boson.

The girls — physics students from the North Carolina School of Science and Mathematics (NCSSM) — log their analysis of the lines and move on to another set. They aren’t getting too excited about their possible Z-boson discovery yet because they still have 48 other sets of lines, or events, to analyze.

Once they’ve worked through all the events, they’ll know if what they’ve seen could be due to a Z-boson decaying into pairs of electrons or muons.

“This exercise isn’t that much different than what scientists do to look for Higgs bosons,” said Duke physicist Mark Kruse, adding that the exercise is a good illustration of the particle-hunting process. “It shows you that you can’t just look at a single event and say ‘that’s a Higgs boson’.”

Kruse shared this insight with the two girls and a dozen other NCSSM high-schoolers during a Large Hadron Collider (LHC) Masterclass held at Duke on March 16. The European Particle Physics Outreach Group runs the masterclasses annually with help from university professors such as Kruse. This was the first time Duke hosted the program for local students.

During the day, they got an introduction to particle physics and research at the LHC and an overview of ATLAS, the experiment Kruse and his collaborators use to search for Higgs bosons and other particles. Then, after a tour of Duke’s Free Electron Laser facility and a pizza lunch, the high-schoolers got their hands on real LHC data.

NCSSM students work on LHC data to find hints of Z-bosons. Credit: Ashley Yeager, Duke

NCSSM students work on LHC data to find hints of Z-bosons. Credit: Ashley Yeager, Duke

They were looking mainly for events that showed possible remnants of a Z-boson. But a few Higgs-like candidates were thrown in too, which excited the students, Kruse and his two graduate students David Bjergaard and Kevin Finelli. The group may have even found a Higgs candidate in one of the first event analyses they looked at during the day.

But, as with all discoveries, they had to take a closer look at their analyses and share their work with others. The group closed the day with a videoconference with high-schoolers in Medellin, Colombia who also went through an LHC masterclass at the same time.

“This was an impressive group. They asked a lot of great questions, sparking some incredible discussion,” Kruse said. The questions — like, does anything make up a quark — are ones other audiences are perhaps too intimidated to ask because they might think it’s a silly question, he said. But it’s these questions that really get everyone thinking about the fundamentals of physics and how much scientists still don’t know, including if quarks can break down into anything smaller. This is in fact one of the many questions LHC scientists are trying to answer.

Based on the success of the class, he is now thinking of running it again for physics students from other area high schools and possibly adapting it for journalists and policymakers. The goal is to illustrate to a wider audience the “gradual, cumulative nature of discovery” at the LHC, he said.

CERN particle ‘a’ Higgs, but not ‘the’ Higgs yet

By Ashley Yeager

This artist's impression shows a proton-proton collision producing a pair of gamma rays, in yellow, in the ATLAS detector at LHC. Credit: CERN.

This artist’s impression shows a proton-proton collision producing a pair of gamma rays, in yellow, in the ATLAS detector at LHC. Credit: CERN.

Scientists say the particle they described in July 2012 is looking more like a Higgs boson. But they can’t yet say much more than that.

Speaking at the Moriond meeting in Italy, researchers using the Large Hadron Collider near Geneva explained their latest analyses show the new particle’s “spin” matches theorists’ predictions for that feature of the Higgs boson.

Physicists want to find a Higgs boson because it would give them clues to the mechanism that gives mass to elementary particles. Finding one specific flavor of the particle would also complete the Standard Model of particle physics, a system that explains how the smallest particles and forces interact to run the universe.

“The updates show this particle is Standard Model-like, but my personal feeling is we can’t yet call it ‘the’ Standard-Model Higgs,” says Duke physicist Mark Kruse who works on one of the Higgs-hunting experiments at CERN. “For one, we believe the Standard Model is wrong.”

The model, he says, does not predict a candidate for dark matter, a form of mass that scientists can’t yet describe. And, he adds, even if the particle’s characteristics, such as spin, match those of the Standard-Model Higgs, scientists can’t yet rule out other theories that also contain Higgs particles with properties similar to the Standard-Model Higgs.

“All we can really say is that this particle is ‘a’ Higgs boson, but not necessarily ‘the’ Standard-Model Higgs,” Kruse says. “We have a lot more to understand and a lot of future research to acquire that understanding.”

Meat Glue — True to its Name

By Ashley Yeager

This is the third post in a four-part, monthly series that gives readers recipes to try in their kitchens and learn a little chemistry and physics along the way. Read the first post here and the second one here.

fish checkerboard

Students grab chunks of a fish “checkerboard” made from salmon and flounder cubes. Credit: Ashley Yeager, Duke.

Braided steak and checkerboard fish may sound exotic. But, freshmen in the Chemistry and Physics of Cooking had no fear fingering the meaty masterpieces into their mouths.

The students made this food art – one literally a braid of three steak strips and the other a combination of salmon and flounder cubes – using a molecule called transglutaminase, also known as meat glue.

In 2012, the media roasted meat glue’s reputation, branding it a dirty little secret meat vendors use to stick together cheap cuts of beef, lamb, chicken or fish and then sell as premium cuts.

“In this class, we’re not using the molecule to be dishonest. We’re using it to be creative,” said physical chemist Patrick Charbonneau, who leads the freshman seminar along with chef Justine de Valicourt and teaching fellows Mary Jane Simpson and Keely Glass.

During a lecture, Glass explained how meat glue — an enzyme that speeds chemical reactions — forms covalent bonds between some of the amino acids that make up the proteins in meat and meat substitutes. With just a sprinkle of the enzyme, which comes in a powder form, chefs can then weave together beef cuts, form game-piece patterns from fish or even bind beans, seeds and other ingredients into a veggie burger that doesn’t crumble after the first bite.

“Meat glue is like a lot of modern ingredients. It comes from industry, and you can use it to make industrial food,” like chicken nuggets, de Valicourt said. “But when you master it, you can use it in a very creative and delicious way.”

Chefs often use the fundamentals of chemistry and physics to shape other foods, such as chocolate. “We’re doing the same to shape meat,” Charbonneau said, explaining that the students used transglutaminase in lab to create beautiful, and delicious, combinations of meat far superior to chicken nuggets and other industrial food typically made with the enzyme.

To make your own meat masterpieces, try the following recipe:


1 long sheet of plastic wrap OR a bowl
1 cutting board
1 knife
2 latex gloves for each person
1 mask for each person
1 meat grinder (optional)
1-3 gallon-sized Ziploc bags
1 scale


1 portion fish, chicken, beef OR vegetarian protein (ie black beans and sunflower seeds)
10 g meat glue powder (available online here)


Gluing meat chucks together –

1. Choose meats
2. Place meat on plastic wrap
3. Choose meat pattern – braid or stack
4. Season meat with salt and pepper
5. Put on gloves and mask and measure 10 g of meat glue using the scale
6. Sprinkle meat glue on sides of meat you want to connect
7. Fold meat into desired pattern
8. Place meat in Ziploc bag
9. Refrigerate for 6 hours
10. Cook meat as you would any other time

Making meat patties –

1. Choose meats, grind in meat grinder, and mix in a bowl (Or, buy ground meat and mix)
2. Season meat with salt and pepper
3. Put on gloves and mask, then measure 10 g of meat glue using the scale
4. Add meat glue to meat and knead until fully mixed
5. Separate into two portions (or more for patties) and seal each in a Ziploc bag
6. Roll with rolling pin, if desired
7. Refrigerate for 6 hours
8. Cook meat as you would any other time

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