Thursday, March 31, 2011

Patterns found in laboratory spark insight into nature and society

Irv Epstein's research is proving that patterns found in mathematical formulas and chemical reactions may be used to understand economics, how an epidemic might spread and the way animal populations survive in the natural world.

Irv Epstein is fascinated with patterns — how they show up in economics, in the coats of animals and within social systems.

“If you look for patterns in social systems, you see them in housing, segregation or in how an epidemic might spread,” says Epstein, the Henry F. Fischbach Professor of Chemistry. “In general, changes don’t occur smoothly, but in patterns that often have some regularity to them.”

While his research is done in the lab, it is proving that and mathematical formulas may also be used to understand how organisms move and the way animal populations survive in the natural world.

Epstein’s group studies oscillatory chemical reactions (systems in which concentrations of various chemical increase and decrease over time); cross-diffusion, spatial pattern formation, transformation of chemical into mechanical energy, dynamical systems and neurobiology. He is the former dean of arts and sciences and provost at Brandeis. He’s also a founder of the Science Posse, which brings underrepresented and economically disadvantaged students to Brandeis to study science.

Hired in 1971 to teach quantum mechanics, Epstein says his interest in oscillating reactions came about while working with some eager undergraduates who were looking for a summer project. Feeling that quantum mechanics would be a bit too complex for students who had just finished their freshman year, he recalled an article in the Journal of Chemical Education about oscillating chemical reactions and suggested the topic.

Little did he know the project would reroute his career.

“One of the students discovered something that contradicted a statement in the classic literature and figured out what was going on,” says Epstein. “We published a paper and I became more interested in this stuff, eventually changing fields completely.”

Epstein says non-linear dynamics and exotic reactions like oscillating chemical reactions are quite rare in chemistry but very important in biology, because every living system is full of reactions in which concentrations increase and decrease, typically on a daily cycle. Unraveling this phenomenon in chemistry is offering insights into pattern formation in other systems, such as human and animal populations.? To better understand diffusion, cross-diffusion and oscillatory chemical reactions, Epstein revisits a science demo popular with the elementary school set: The glass of water and drop of food coloring.
Diffusion is the phenomenon by which a species spreads out from a concentrated region to a less concentrated region. When a drop of red food coloring is placed in a glass of water, the food coloring disperses over time, resulting in a uniform pink glass of colored water. The process by which the color spreads is diffusion.

Cross-diffusion is a process in which two species are spreading- for example, if you have both a red drop and a blue drop of food coloring; the “cross” aspect means that the distribution of one color affects the diffusion of the other.

“Chemists and physicists have largely ignored cross-diffusion,” says Epstein. “When you study diffusion in an introductory chemistry or physics course, the standard treatment completely ignores the possibility that if there are two different chemicals present one might influence the diffusion of the other.”

Using his theories, Epstein is creating mathematical models to use in the context of biological, ecological and social systems.

“Instead of having blue molecules and red molecules, maybe you have populations of two different ethnic groups that either like to be near each other or prefer to avoid each other,” says Epstein. “This might affect population patterns in a city or region.”

While he’s not expecting urban planners to track him down this year, his research is gaining momentum.

In ecology, Epstein says, one can create models to describe a predator-prey system.

“Suppose I have foxes and rabbits,” says Epstein. “If the rabbits are by themselves, they’ll distribute evenly, assuming that the food supply is evenly distributed. But if I introduce foxes into the system, then the foxes will eat the rabbits and the rabbits will tend to move away from high concentrations of foxes.” You can actually [design] a mathematical model that describes the processes by which rabbits eat grass and multiply, foxes eat rabbits and multiply and the two species move around.”

While many of the exotic reactions that Epstein examines touch on oscillation and transience, Epstein himself is an example of steadfastness.

Epstein has spent this year at Harvard as Radcliffe Institute Fellow, but he has literally spent his adult life at Brandeis. He arrived in 1971 during the bitter end of the Vietnam War, experienced the ‘80s with the explosion of the space shuttle Challenger and the discovery of AIDS, the ‘90s with the release of Nelson Mandela, the end of the Cold War and the dawn of the 21st century, where smart phones and social media have changed the way people live their lives.
As Epstein points out, the lab facilities at Brandeis have evolved as well.

“When I started at Brandeis,” he says, “ I had only a small office and no labs. As I shifted my efforts from theory to experiment, generous colleagues offered to share lab space with me, and I eventually inherited labs of my own when they retired, but the space was less than ideal.”

Two years ago his research team moved to the newly constructed Shapiro Science Center, where, for the first time, Epstein says, they can control key variables such as room temperature and lighting levels without having to resort to Rube Goldberg-like “fixes.”

A native of Queens, N.Y., Epstein was an only child. His father was a locksmith born in Russia, his mother a school librarian. He earned a B.A. in chemistry and physics, an M.A. in chemistry and a Ph.D. in chemical physics from Harvard University and a diploma in advanced mathematics as a Marshall Scholar at the University of Oxford. After a NATO post-doctoral fellowship at the University of Cambridge, he moved from England to New England, accepting a position at Brandeis.

Twenty-one years later, Epstein was made dean of arts and sciences, moving up to provost in 1994 when the incumbent provost, Jehuda Reinharz, became Brandeis’ seventh president.

Robin Feuer Miller, professor of Russian literature who served as dean of arts and sciences from 1994-2000, worked closely with Epstein during his seven- year term as provost.

“He is, quite simply, one of the smartest people I know,” says Miller. “But what I perhaps valued most about working with him was his ability to change his mind” after making an effort to understand another side.
On the occasions when they disagreed, Miller said, they were always able to talk things through and come to an amicable decision.

Perhaps it’s this passion for people and progress that played into Epstein’s success in garnering a million-dollar grant in 2006 from the Howard Hughes Medical Institute (HHMI), the nation’s largest private funder of science education, to start the first Science Posse, a program at Brandeis created to attract and retain talented, underrepresented students in college-level science.

“If you look at the statistics, the state of American science, we are falling behind,? says Epstein. “More than half of the graduate students in chemistry, math and physics are from other countries. And if you look even more closely, underrepresented minorities are even more underrepresented in the sciences.”

In 2010, the foundation awarded an additional $600,000 to further develop the program. The Science Posse is an extension of the successful Posse Foundation, a liberal arts program founded in 1989 by Brandeis alum Deborah Bial ‘87, which carefully selects and trains a group or “posse” of students who act as a support system for each other.

Though the students don’t know each other when they’re chosen, between the time that they’re selected in December and when they arrive on campus in September, they will have spent 3-4 hours a week together, bonding and learning skills from time management to persuasive writing.

“Irv has vision,” says assistant biology professor Melissa Kosinski-Collins who runs the academic side of the Science Posse as well as the summer boot camp. “He genuinely cares about our scholars and makes it his goal to be there when they need him.”

Jerry Saunders II ‘11 is a member of the Science Posse. He said that working in Epstein’s lab was one of the highlights of his undergraduate career.

“Dr. Epstein is a real-time celebrity whose example constantly challenges me to always strive for more,” says Saunders. “Despite his many successes he remains interested in the work you are doing and what you hope to accomplish. Furthermore, he is more than willing to assist you in that path. He is never too busy to lend guidance.”

Eve Marder, head of division of science and the Victor and Gwendolyn Beinfield Professor of Neuroscience, got to know Epstein in the late 1980s when the pair collaborated on building a semi-realistic model of a neuro-oscilator; in other words, they developed mathematical models used to research several kinds of neurons that are studied in Marder’s lab.

“He was doing the theory and we went back and forth discussing the biology,” says Marder. The two also wrote a grant together.

“Irv has got to be the fastest writer and fastest and best editor that I’ve ever worked with,” says Marder. “He’s astronomically quick. I think that’s part of the reason that he’s been so successful and productive.”

More information: http://pubs.acs.or … eda8/current

Provided by Brandeis University (news : web)

Biosensors: Hormonal attractions

Estrogen receptor (ER) proteins play a major role in controlling the transcription of genetic information from DNA to messenger RNA in cells. Understanding how ER proteins interact with specific DNA regulatory sequences may shed new light on important physiological processes in the body, such as cell growth and differentiation, as well as the development and progression of breast cancer. Guo-Jun Zhang at the A*STAR Institute of Microelectronics and co-workers have now developed a detector that uses silicon nanowires (SiNWs) to evaluate these interactions.

The magnitude of the transcriptional activity that arises from the ER–DNA binding varies from one gene to another. Some genes are highly affected while others are only marginally changed. Zhang and his co-workers therefore investigated how slight variations in nucleotide composition affect the binding affinity between ER and DNA. By combining this new information with existing experimental data on gene expression, the researchers could predict transcriptional outcome following ER–DNA binding and gain new insight into ER signaling.

Most imaging techniques developed for the study of interactions between ER proteins and DNA targets are time-consuming and require the use of fluorescent labels. A number of label-free methods exist, but they lack the sensitivity needed to distinguish subtle changes in ER–DNA binding. The new system created by Zhang’s team is both label-free and highly sensitive.

The researchers prepared their ER-based sensor by modifying a nanostructured biosensing platform previously used to detect cardiac biomarkers and the dengue virus. They generated SiNW arrays on a silica substrate (pictured) through optical lithography and covered the silicon surfaces with functional organosilane and organic molecules, which allowed them to immobilize the ER proteins on the . Next, a well-shaped sample holder, constructed of insulating material, was pasted around the SiNW area.

After exposing the ER-functionalized nanowires with the target DNA, the team measured the change in resistance induced by ER–DNA complex formation to assess the binding affinity. Upon binding to ERs, DNA strands increased the overall increase in resistance of the SiNWs by adding negative charges.

The researchers discovered that the sensor could detect ultralow levels of ER-bound DNA and discriminate ER-specific from mutant DNA sequences. Moreover, the DNA easily detached from the ER-functionalized nanowires upon contact with a detergent, enabling the regeneration of the sensor.

“The SiNW array biosensor platform is now helping us in the multiplexed characterization of interactions,” says Zhang.

More information: Zhang, G.-J. et al. Highly sensitive and reversible silicon nanowire biosensor to study nuclear hormone receptor protein and response element DNA interactions. Biosensors and Bioelectronics 26, 365–370 (2010). … .2010.07.129

Provided by Agency for Science, Technology and Research (A*STAR)

Swedish invention simplifies home diagnostics

Advances in medical diagnostic technology will likely allow individuals to perform preliminary medical diagnoses themselves, in their own home, in the future.

"The idea is to make complex diagnostic processes as simple to perform as modern-day pregnancy tests," says Nathaniel Robinson, who leads the Transport and Separations Group at Linköping University in Sweden

Dr. Robinson and PhD student Per Erlandsson have invented an improved pump, called an electroosmotic pump, which can be placed in a "microfluidic chip." Such chips, sometimes called "lab-on-a-chip" devices, contain miniaturized versions of the beakers and test tubes found in chemistry laboratories interconnected by tiny pipes. Rather than using moving parts, the new pump moves fluids in these pipes via an electric current. The fluids to be pumped can be biological samples such as blood, urine or saliva for medical devices.

"The trick is to generate the ionic current that moves the fluid to be pumped without disturbing the cells, proteins, and other molecules in the sample," according to Dr. Robinson.

To do this, the researchers have employed a type of electronically conducting plastic in the pump's electrodes. The plastic can be electrochemically oxidized or reduced, acting as a transducer between the ions, the charge carriers in fluids, and electrons, which carry charge in metal wires. Traditional electroosmotic pumps use metal electrodes and the electrochemical reactions required are performed on the water in the sample itself. By-products of this electrochemistry included oxygen and hydrogen gas bubbles, and the production of acid or base. Each of these by-products disturbs the microfluidic device and the fluid sample.

"This is primarily why electroosmotic pumps have not been more widely used in the development of medical devices," says Robinson.

The researchers have shown that the pump can be operated repeatedly for extended periods of time, and can operate at relatively low voltages, so that small, portable diagnostic devices can be driven by batteries.

"Several microfluidics articles describe ways to work around the complications associated with integrated metal-electrodes. Here, the alternative reactions of electrochemically active electrodes give us the chance to remove the core problem, the electrolysis of solvent," according to Per Erlandsson, who constructed the pumps.

The researchers have applied for a patent for the new invention and are currently looking for partners who have a need for such pumps in their lab-on-a-chip devices. The research is also described in an article appearing in the latest issue of the scientific journal Electrophoresis.

Simple-to-operate medical devices, that will ultimately enable preliminary self-diagnosis via automated testing kits, will likely become an important part of our healthcare system. Otherwise, we will have a difficult time financing healthcare for an aging population at current or expanded levels of service. For example, by automating and simplifying screening for diseases, such as cancer, a greater portion of the population can be screened, more cases will be caught early, and hospital resources can focus on treatment of individuals who are truly ill. This pump is a significant step towards realizing the devices that will make this possible.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Expertanswer (Expertsvar in Swedish), via AlphaGalileo.

Journal Reference:

Per G. Erlandsson, Nathaniel D. Robinson. Electrolysis-reducing electrodes for electrokinetic devices. Electrophoresis, 2011; 32 (6-7): 784 DOI: 10.1002/elps.201000617

Global water experiment will celebrate the International Year of Chemistry 2011

What may be the world's largest chemistry experiment in history launched last week as part of the International Year of Chemistry 2011. The American Chemical Society (ACS) announced it will help support teachers and students who wish to participate in the experiment, "Water: A Chemical Solution," by sending volunteers to classrooms that need assistance.

In 2011, as part of the International Year of Chemistry (IYC), officially designated by the United Nations, students worldwide will test their local drinking water sources, as well as local lakes, rivers, streams and other bodies of water, and post their analysis to a global, internet data map.

The experiment remains open until Dec. 31, 2011. Teachers, scout leaders, and families can register to participate, view the experiments, and enter their results at: The activities are suitable for students of all ages from kindergarten to high school, and require materials commonly found in most science classrooms.

Students will conduct four tests to analyze their water resources for characteristics critical to providing clean drinking water and will learn essential water chemistry practices. They will test the acidity and salinity of their water, and perform simple water treatment and desalinization procedures.

Clean drinking water is one the most important resources for human health and survival. The most abundant substance on the Earth's surface, water covers about 70 percent of the planet's surface. It also constitutes about 70 percent of the human body. Important as it is, water quality varies greatly from community to community for a wide variety of reasons including landscape, weather, temperature and human impacts.

A global comparison of water resources will open important discussions and insights into a precious natural resource and how people in different environments use various methods to provide clean, safe drinking water.

"Students learn chemistry best when it directly applies to their lives," said ACS President, Nancy B. Jackson, Ph.D. "And the most basic chemical solution is water. But don't let that fool you – water resource quality opens complex and diverse issues. The global experiment is an important science education initiative."

Other U.S. organizations helping to coordinate the global experiment include the American Chemical Council (ACC) and the National Academy of Sciences.

The United Nations Educational, Scientific and Cultural Organization (UNESCO), together with the International Union of Pure and Applied Chemistry (IUPAC) officially designated 2011 as the International Year of . In addition to the global experiment, a wide range of celebrations, science conferences, school projects, and community events worldwide are planned for IYC 2011.

Provided by American Chemical Society (news : web)

New trash-to-treasure process turns landfill nuisance into plastic

With billions of pounds of meat and bone meal going to waste in landfills after a government ban on its use in cattle feed, scientists today described development of a process for using that so-called meat and bone meal to make partially biodegradable plastic that does not require raw materials made from oil or natural gas. They reported here today at the 241st National Meeting and Exposition of the American Chemical Society (ACS).

Fehime Vatansever and colleagues explained that in 1997, the U. S banned the decades-old practice of feeding meat and bone meal (MBM) made from of slaughtered cattle, sheep, and farmed deer, elk and bison to those same animals. Other countries took similar action. It stemmed from concern over the human form of , a very rare but fatal brain disorder that spread in the United Kingdom from eating infected meat. As of 2010, only three cases of the disease, (BSE), had occurred in the United States. The bans were to reduce the chances that meat and bone meal made from one infected cow could spread BSE widely throughout cattle herds.

"The ban changed what once was a valuable resource — a nutritious component of cattle feed — into waste disposal headache," Vatansever said. "More than nine billion pounds of protein meal are produced by the U.S. rendering industry each year, and most of that is meat and bone meal. The meal from cows had to be treated with harsh chemicals to destroy any BSE and then put into special landfills. We thought we could keep meat and bone meal from being deposited in landfills by using it to make petroleum-free bioplastics."

Vatansever and her colleagues described development and successful testing of that process, which uses meat and bone as the raw material rather than the chemical compounds in petroleum or natural gas. They mixed the MBM plastic with so-called ultra-high-molecular weight polyethylene (UHMWPE), an extremely tough plastic used in skis, snowboards, joint replacements, PVC windows, and other products. Their tests showed that the MBM/UHMWPE plastic is almost as durable as UHMWPE with the bonus of being partially biodegradable.

Any of the BSE infectious agents that might be present in meat and bone meal are deactivated during the manufacture of the , Vatansever noted.

"This is just one way to reuse meat and bone meal, and it's great because it reduces the amount of petroleum needed to make plastics," Vatansever said. "We've also managed to create a strong, sustainable material that is easy to manufacture."

Provided by American Chemical Society (news : web)

Major advance in understanding how nanowires form

New insights into why and how nanowires take the form they do promise to have profound implications for the development of future electronic components. PhD student Peter Krogstrup from the Nano-Science Center at the University of Copenhagen is behind the new theoretical model, which is developed in collaboration with researchers from CINAM-CNRS in Marseille.

One of the most important components in future electronic devices will likely be based on nanocrystals, which are smaller than the wavelength of the light our eyes can detect. Nanowires, which are extremely thin nanocrystal wires, are predicted to have a predominant role in these technologies because of their unique electrical and optical properties. Researchers around the world have been working for years to improve the properties of these nanowires.

With his research, PhD student Peter Krogstrup at the Niels Bohr Institute, University of Copenhagen has laid the foundations for a greater understanding of nanowires. With that comes the potential for improving their performance, which will bring the research closer to being applied in the development of solar cells and computers. In the latest edition of Physical Review Letters, he describes how, under certain conditions, nanowires form a crystal structure that really should not be possible, seen from an energy perspective.

"Crystals will always try to take the form in which their internal energy is as little as possible. It is a basic law of physics and according to it these nanowires should have a cubic crystal structure, but we almost always see that a large part of the structure is hexagonal," explains Peter Krogstrup, who has been working with the theory in recent years.

Catalyst particle shape is the key

In order to explain why and when these crystals become hexagonal, Peter Krogstrup has, as part of his doctoral dissertation, examined the shape of the catalyst particle (a little nano-droplet), which controls the growth of the nanowires. It appears that the shape of the droplet depends on the amount of atoms from group 3 in the periodic system, which make up half of the atoms in the nanowire crystal. The other half, atoms from group 5 in the periodic system, are absorbed by the drop and hence the atoms organize themselves into a lattice, and the nanowire crystal will grow.

"We have shown that it is the shape of the droplet, which determines what kind of crystal structure the nanowires obtain and with this knowledge it will be easier to improve the properties of the nanowires," explains Peter Krogstrup and continues: "The crystal structure has an enormous influence on the electrical and optical properties of the nanowires and you would typically want them to have a certain structure, either cubic or hexagonal. The better nanowires we can make the better electronic components we can make to the benefit of us all," says Peter Krogstrup, whose research is conducted in collaboration with the firm SunFlake A/S, which is located at the Nano-Science Center at the University of Copenhagen. The company is working to develop solar cells of the future based on nanowires.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by University of Copenhagen, via EurekAlert!, a service of AAAS.

Journal Reference:

Peter Krogstrup, Stefano Curiotto, Erik Johnson, Martin Aagesen, Jesper Nygard, Dominique Chatain. Impact of the Liquid Phase Shape on the Structure of III-V Nanowires. Physical Review Letters, 2011; 106 (12) DOI: 10.1103/PhysRevLett.106.125505

Twinkle, twinkle, quantum dot: New particles can change colors and tag molecules

 Engineers at Ohio State University have invented a new kind of nano-particle that shines in different colors to tag molecules in biomedical tests.

These tiny plastic nano-particles are stuffed with even tinier bits of electronics called quantum dots. Like little traffic lights, the particles glow brightly in red, yellow, or green, so researchers can easily track molecules under a microscope.

This is the first time anyone has created fluorescent nano-particles that can change colors continuously.

Jessica Winter, assistant professor of chemical and biomolecular engineering and biomedical engineering, and research scientist Gang Ruan describe their patent-pending technology in the online edition of the journal Nano Letters.

Researchers routinely tag molecules with fluorescent materials in order to see them under the microscope. Unlike the more common fluorescent molecules, quantum dots shine very brightly, and could illuminate chemical reactions especially well, allowing researchers to see the inner workings of living cells.

A bottleneck to combating major diseases like cancer is the lack of molecular or cellular-level understanding of biological processes, the engineers explained.

"These new nanoparticles could be a great addition to the arsenal of biomedical engineers who are trying to find the roots of diseases," Ruan said.

"We can tailor these particles to tag particular molecules, and use the colors to track processes that we wouldn't otherwise be able to," he continued. "Also, this work could be groundbreaking for the field of nanotechnology as a whole, because it solves two seemingly irreconcilable problems with using quantum dots."

Quantum dots are pieces of semiconductor that measure only a few nanometers, or billionths of a meter, across. They are not visible to the naked eye, but when light shines on them, they absorb energy and begin to glow. That's what makes them good tags for molecules.

Due to quantum mechanical effects, quantum dots "twinkle" -- they blink on and off at random moments. When many dots come together, however, their random blinking is less noticeable. So, large clusters of quantum dots appear to glow with a steady light.

Blinking has been a problem for researchers, because it breaks up the trajectory of a moving particle or tagged molecule that they are trying to follow. Yet, blinking is also beneficial, because when dots come together and the blinking disappears, researchers know for certain that tagged molecules have aggregated.

"Blinking is good and bad," Ruan explained. "But one day we realized that we could use the 'good' and avoid the 'bad' at the same time, by grouping a few quantum dots of different colors together inside a micelle."

A micelle is a nano-sized spherical container, and while micelles are useful for laboratory experiments, they are easily found in household detergents -- soap forms micelles that capture oils in water. Ruan created micelles using polymers, with different combinations of red and green quantum dots inside them.

In tests, he confirmed that the micelles appeared to glow steadily. Those stuffed with only red quantum dots glowed red, and those stuffed with green glowed green. But those he stuffed with red and green dots alternated from red to green to yellow.

The color change happens when one or another dot blinks inside the micelle. When a red dot blinks off and the green blinks on, the micelle glows green. When the green blinks off and the red blinks on, the micelle glows red. If both are lit up, the micelle glows yellow.

The yellow color is due to our eyes' perception of light. The process is the same as when a red pixel and green pixel appear close together on a television or computer screen: our eyes see yellow.

Nobody can control when color changes happen inside individual micelles. But because the particles glow continuously, researchers can use them to track tagged molecules continuously. They can also monitor color changes to detect when molecules come together.

Winter and Ruan said that the particles could also be used in fluid mechanics research -- specifically, micro-fluidics. Researchers who are developing tiny medical devices with fluid separation channels could use quantum dots to follow the fluid's path.

The same Ohio State research team is also developing magnetic particles to enhance medical imaging of cancer, and it may be possible to combine magnetism with the quantum dot technology for different kinds of imaging. But before the particles would be safe to use in the body, they would have to be made of biocompatible materials. Carbon-based nanomaterials are one possible option.

In the meantime, Winter and Ruan are going to continue developing the color-changing quantum dot particles for studies of cells and molecules under the microscope. They are also going to explore what happens when quantum dots of another color -- for instance, blue -- are added to the mix.

The university will look to license the technology for industry, and Winter and Ruan have created a Web site for the technologies they are developing:

This research was supported by the National Science Foundation, an endowment from the William G. Lowrie family to the Department of Chemical and Biomolecular Engineering, and the Center for Emergent Materials at Ohio State.

Story Source:

The above story is reprinted (with editorial adaptations) from materials provided by Ohio State University. The original article was written by Pam Frost Gorder.

Journal Reference:

Gang Ruan, Jessica O. Winter. Alternating-Color Quantum Dot Nanocomposites for Particle Tracking. Nano Letters, 2011; 11 (3): 941 DOI: 10.1021/nl103233b