An improvement to the global software standard for analyzing fusion plasmas (Nuclear Fusion)

Posted on by Catherine Zandonella

By Raphael Rosen, Princeton Plasma Physics Laboratory

The gold standard for analyzing the behavior of fusion plasmas may have just gotten better. Mario Podestà, a staff physicist at the U.S. Department of Energy’s Princeton Plasma Physics Laboratory (PPPL), has updated the worldwide computer program known as TRANSP to better simulate the interaction between energetic particles and instabilities – disturbances in plasma that can halt fusion reactions. The program’s updates, reported in the journal Nuclear Fusion, could lead to improved capability for predicting the effects of some types of instabilities in future facilities such as ITER, the international experiment under construction in France to demonstrate the feasibility of fusion power.

Podestà and co-authors saw a need for better modeling techniques when they noticed that while TRANSP could accurately simulate an entire plasma discharge, the code wasn’t able to represent properly the interaction between energetic particles and instabilities. The reason was that TRANSP, which PPPL developed and has regularly updated, treated all fast-moving particles within the plasma the same way. Those instabilities, however, can affect different parts of the plasma in different ways through so-called “resonant processes.”

The authors first figured out how to condense information from other codes that do model the interaction accurately – albeit over short time periods – so that TRANSP could incorporate that information into its simulations. Podestà then teamed up with TRANSP developer Marina Gorelenkova at PPPL to update a TRANSP module called NUBEAM to enable it to make sense of this condensed data. “Once validated, the updated module will provide a better and more accurate way to compute the transport of energetic particles,” said Podestà. “Having a more accurate description of the particle interactions with instabilities can improve the fidelity of the program’s simulations.”

Schematic of NSTX tokamak at PPPL with a cross-section showing perturbations of the plasma profiles caused by instabilities. Without instabilities, energetic particles would follow closed trajectories and stay confined inside the plasma (blue orbit). With instabilities, trajectories can be modified and some particles may eventually be pushed out of the plasma boundary and lost (red orbit). Credit: Mario Podestà
Schematic of NSTX tokamak at PPPL with a cross-section showing perturbations of the plasma profiles caused by instabilities. Without instabilities, energetic particles would follow closed trajectories and stay confined inside the plasma (blue orbit). With instabilities, trajectories can be modified and some particles may eventually be pushed out of the plasma boundary and lost (red orbit). Credit: Mario Podestà

Fast-moving particles, which result from neutral beam injection into tokamak plasmas, cause the instabilities that the updated code models. These particles begin their lives with a neutral charge but turn into negatively charged electrons and positively charged ions – or atomic nuclei – inside the plasma. This scheme is used to heat the plasma and to drive part of the electric current that completes the magnetic field confining the plasma.

The improved simulation tool may have applications for ITER, which will use fusion end-products called alpha particles to sustain high plasma temperatures. But just like the neutral beam particles in current-day-tokamaks, alpha particles could cause instabilities that degrade the yield of fusion reactions. “In present research devices, only very few, if any, alpha particles are generated,” said Podestà. “So we have to study and understand the effects of energetic ions from neutral beam injectors as a proxy for what will happen in future fusion reactors.”

PPPL, on Princeton University’s Forrestal Campus in Plainsboro, N.J., is devoted to creating new knowledge about the physics of plasmas — ultra-hot, charged gases — and to developing practical solutions for the creation of fusion energy. Results of PPPL research have ranged from a portable nuclear materials detector for anti-terrorist use to universally employed computer codes for analyzing and predicting the outcome of fusion experiments. The Laboratory is managed by the University for the U.S. Department of Energy’s Office of Science, which is the largest single supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, visit science.energy.gov.

Read the paper

Podestà, M. Gorelenkova, D.S. Darrow, E.D. Fredrickson, S.P. Gerhardt and R.B. White. Nucl. Fusion 55 053018
doi:10.1088/0029-5515/55/5/053018

Decoding the Cell’s Genetic Filing System (Nature Chemistry)

Posted on by Catherine Zandonella

By Tien Nguyen, Department of Chemistry

A fully extended strand of human DNA measures about five feet in length. Yet it occupies a space just one-tenth of a cell by wrapping itself around histones—spool-like proteins—to form a dense hub of information called chromatin.

Access to these meticulously packed genes is regulated by post-translational modifications, chemical changes to the structure of histones that act as on-off signals for gene transcription. Mistakes or mutations in histones can cause diseases such as glioblastoma, a devastating pediatric brain cancer.

Source: Nature Chemistry
Source: Nature Chemistry

Researchers at Princeton University have developed a facile method to introduce non-native chromatin into cells to interrogate these signaling pathways. Published on April 6 in the journal Nature Chemistry, this work is the latest chemical contribution from the Muir lab towards understanding nature’s remarkable information indexing system.

Tom Muir, the Van Zandt Williams, Jr. Class of ’65 Professor of Chemistry, began investigating transcriptional pathways in the so-called field of epigenetics almost a decade earlier. Deciphering such a complex and dynamic system posed a formidable challenge, but his research lab was undeterred. “It’s better to fail at something important than to succeed at something trivial,” he said.

Muir recognized the value of introducing chemical approaches to epigenetics to complement early contributions that came mainly from molecular biologists and geneticists. If epigenetics was like a play, he said, molecular biology and genetics could identify the characters but chemistry was needed to understand the subplots.

These subplots, or post-translational modifications of histones, of which there are more than 100, can occur cooperatively and simultaneously. Traditional methods to probe post-translational modifications involved synthesizing modified histones one at a time, which was a very slow process that required large amounts of biological material.

Last year, the Muir group introduced a method that would massively accelerate this process. The researchers generated a library of 54 nucleosomes—single units of chromatin, like pearls on a necklace—encoded with DNA-barcodes, unique genetic tags that can be easily identified. Published in the journal Nature Methods, the high throughput method required only microgram amounts of each nucleosome to run approximately 4,500 biochemical assays.

“The speed and sensitivity of the assay was shocking,” Muir said. Each biochemical assay involved treatment of the DNA-barcoded nucleosome with a writer, reader or nuclear extract, to reveal a particular binding preference of the histone. The products were then isolated using a technique called chromatin immunoprecipitation and characterized by DNA sequencing, essentially an ordered readout of the nucleotides.

“There have been incredible advances in genetic sequencing over the last 10 years that have made this work possible,” said Manuel Müller, a postdoctoral researcher in the Muir lab and co-author on the Nature Methods article.

Schematic of approach using split inteins
Schematic of approach using split inteins

With this method, researchers could systematically interrogate the signaling system to propose mechanistic pathways. But these mechanistic insights would remain hypotheses unless they could be validated in vivo, meaning inside the cellular environment.

The only method for modifying histones in vivo was extremely complicated and specific, said Yael David, a postdoctoral researcher in the Muir lab and lead author on the recent Nature Chemistry study that demonstrated a new and easily customizable approach.

The method relied on using ultra-fast split inteins, protein fragments that have a great affinity for one another. First, one intein fragment was attached to a modified histone, by encoding it into a cell. Then, the other intein fragment was synthetically fused to a label, which could be a small protein tag, fluorophore or even an entire protein like ubiquitin.

Within minutes of being introduced into the cell, the labeled intein fragment bound to the histone intein fragment. Then like efficient and courteous matchmakers, the inteins excised themselves and created a new bond between the label and modified histone. “It’s really a beautiful way to engineer proteins in a cell,” David said.

Regions of the histone may be loosely or tightly packed, depending on signals from the cell indicating whether or not to transcribe a gene. By gradually lowering the amount of labeled intein introduced, the researchers could learn about the structure of chromatin and tease out which areas were more accessible than others.

Future plans in the Muir lab will employ these methods to ask specific biological questions, such as whether disease outcomes can be altered by manipulating signaling pathway. “Ultimately, we’re developing methods at the service of biological questions,” Muir said.

This research was supported by the US National Institutes of Health (grants R37-GM086868 and R01 GM107047).

Read the articles:

Nguyen, U.T.T.; Bittova, L.; Müller, M.; Fierz, B.; David, Y.; Houck-Loomis, B.; Feng, V.; Dann, G.P.; Muir, T.W. “Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries.” Nature Methods, 2014, 11, 834.

David, Y.; Vila-Perelló, M; Verma, S.; Muir, T.W. “Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins.” Nature Chemistry, Advance online publication, April 6, 2015.

Frustrated magnets – new experiment reveals clues to their discontent (Science)

Posted on by Catherine Zandonella

By Catherine Zandonella, Office of the Dean for Research

A crystal of frustrated magnet (Tb2Ti2O7). Image credit: Jason Krizan.
A crystal of frustrated magnet (Tb2Ti2O7). Image credit: Jason Krizan.

An experiment conducted by Princeton researchers has revealed an unlikely behavior in a class of materials called frustrated magnets, addressing a long–debated question about the nature of these discontented quantum materials.

The work represents a surprising discovery that down the road may suggest new research directions for advanced electronics. Published this week in the journal Science, the study also someday may help clarify the mechanism of high-temperature superconductivity, the frictionless transmission of electricity.

The researchers tested the frustrated magnets — so-named because they should be magnetic at low temperatures but aren’t — to see if they exhibit a behavior called the Hall Effect. When a magnetic field is applied to an electric current flowing in a conductor such as a copper ribbon, the current deflects to one side of the ribbon. This deflection, first observed in 1879 by E.H. Hall, is used today in sensors for devices such as computer printers and automobile anti-lock braking systems.

Because the Hall Effect happens in charge-carrying particles, most physicists thought it would be impossible to see such behavior in non-charged, or neutral, particles like those in frustrated magnets. “To talk about the Hall Effect for neutral particles is an oxymoron, a crazy idea,” said N. Phuan Ong, Princeton’s Eugene Higgins Professor of Physics.

Nevertheless, some theorists speculated that the neutral particles in frustrated magnets might bend to the Hall rule under extremely cold conditions, near absolute zero, where particles behave according to the laws of quantum mechanics rather than the classical physical laws we observe in our everyday world. Harnessing quantum behavior could enable game-changing innovations in computing and electronic devices.

Ong and colleague Robert Cava, Princeton’s Russell Wellman Moore Professor of Chemistry, and their graduate students Max Hirschberger and Jason Krizan decided to see if they could settle the debate and demonstrate conclusively that the Hall Effect exists for frustrated magnets.

To do so, the research team turned to a class of the magnets called pyrochlores. They contain magnetic moments that, at very low temperatures near absolute zero, should line up in an orderly manner so that all of their “spins,” a quantum-mechanical property, point in the same direction. Instead, experiments have found that the spins point in random directions. These frustrated materials are also referred to as “quantum spin ice.”

“These materials are very interesting because theorists think the tendency for spins to align is still there, but, due to a concept called geometric frustration, the spins are entangled but not ordered,” Ong said. Entanglement is a key property of quantum systems that researchers hope to harness for building a quantum computer, which could solve problems that today’s computers cannot handle.

A chance conversation in a hallway between Cava and Ong revealed that Cava had the know-how and experimental infrastructure to make such materials. He tasked chemistry graduate student Krizan with growing the crystals while Hirschberger, a graduate student in physics, set up the experiments needed to look for the Hall Effect.

Graduate student Max Hirschberger lowers the assembled experimental setup into a high-field magnet system, capable of creating fields as strong as 250,000 times the earth's magnetic field. (Image credit: Jason Krizan.)
Graduate student Max Hirschberger lowers the assembled experimental setup into a high-field magnet system, capable of creating fields as strong as 250,000 times the earth’s magnetic field. (Image credit: Jason Krizan.)

“The main challenge was how to measure the Hall Effect at an extremely low temperature where the quantum nature of these materials comes out,” Hirschberger said. The experiments were performed at temperatures of 0.5 degrees Kelvin, and required Hirschberger to resolve temperature differences as small as a thousandth of a degree between opposite edges of a crystal.

To grow the crystals, Krizan first synthesized the material from terbium oxide and titanium oxide in a furnace similar to a kiln. After forming the pyrochlore powder into a cylinder suitable for feeding the crystal growth, Krizan suspended it in a chamber filled with pure oxygen and blasted it with enough focused light from four 1000-Watt halogen light bulbs to heat a small region to 1800 degrees Celsius. The final products were thin, flat transparent or orange slabs about the size of a sesame seed.

To test each crystal, Hirschberger attached tiny gold electrodes to either end of the slab, using microheaters to drive a heat current through the crystal. At such low temperatures, this heat current is analogous to the electric current in the ordinary Hall Effect experiment.

At the same time, he applied a magnetic field in the direction perpendicular to the heat current. To his surprise, he saw that the heat current was deflected to one side of the crystal. He had observed the Hall Effect in a non-magnetic material.

Surprised by the results, Ong suggested that Hirschberger repeat the experiment, this time by reversing the direction of the heat current. If Hirschberger was really seeing the Hall Effect, the current should deflect to the opposite side of the crystal. Reconfiguring the experiment at such low temperatures was not easy, but eventually he demonstrated that the signal did indeed reverse in a manner consistent with the Hall Effect.

“All of us were very surprised because we work and play in the classical, non-quantum world,” Ong said. “Quantum behavior can seem very strange, and this is one example where something that shouldn’t happen is really there. It really exists.”

The use of experiments to probe the quantum behavior of materials is essential for broadening our understanding of fundamental physical properties and the eventual exploitation of this understanding in new technologies, according to Cava. “Every technological advance has a basis in fundamental science through our curiosity about how the world works,” he said.

Further experiments on these materials may provide insights into how superconductivity occurs in certain copper-containing materials called cuprates, also known as “high-temperature” superconductors because they work well above the frigid temperatures required for today’s superconductors, such as those used in MRI machines.

One of the ideas for how high-temperature superconductivity could occur is based on the possible existence of a particle called the spinon. Theorists, including the Nobel laureate Philip Anderson, Princeton’s Joseph Henry Professor of Physics, Emeritus and a senior physicist, and others have speculated that spinons could be the carrier of a heat current in a quantum system such as the one explored in the present study.

Although the team does not claim to have observed the spinon, Ong said that the work could lead in such a direction in the future. “This work sets the stage for hunting the spinon,” Ong said. “We have seen its tracks, so to speak.”

 

The research was funded by the Army Research Office (ARO W911NF-11-1-0379, ARO W911NF-12-1-0461), the U.S. National Science Foundation (DMR 1420541), and the U.S. Department of Energy’s Division of Basic Energy Sciences, (DE-FG-02-08ER46544).

Citation:

Max Hirschberger, Jason W. Krizan, R. J. Cava, N. P. Ong. Large thermal Hall conductivity of neutral spin excitations in a frustrated quantum magnet. Science. 10.1126/science.1257340

Revisiting the mechanics of the action potential (Nature Communications)

Posted on by Catherine Zandonella

By Staff

AW_Pic
The action potential (AP) and the accompanying action wave (AW) constitute an electromechanical pulse traveling along the axon.

The action potential is widely understood as an electrical phenomenon. However, a long experimental history has documented the existence of co-propagating mechanical signatures.

In a new paper in the journal Nature Communications, two Princeton University researchers have proposed a theoretical model to explain these mechanical signatures, which they term “action waves.” The research was conducted by Ahmed El Hady, a visiting postdoctoral research associate at the Princeton Neuroscience Institute and a postdoctoral fellow at the Howard Hughes Medical Institute, and Benjamin Machta, an associate research scholar at the Lewis-Sigler Institute for Integrative Genomics and a lecturer in physics and the Lewis-Sigler Institute for Integrative Genomics.

In the model, the co-propagating waves are driven by changes in charge separation across the axonal membrane, just as a speaker uses charge separation to drive sound waves through the air. The researchers argue that these forces drive surface waves involving both the axonal membrane and cytoskeleton as well as its surrounding fluid. Their model may help shed light on the functional role of the surprisingly structured axonal cytoskeleton that recent super-resolution techniques have uncovered, and suggests a wider role for mechanics in neuronal function.

Read the paper.

Ahmed El Hady & Benjamin B. Machta. Mechanical surface waves accompany action potential propagation. Nature Communications 6, No. 6697 doi:10.1038/ncomms7697