Berkeley Lab and University of Wisconsin Researchers Unveil FTIR spectro-microtomography
Researchers at Berkeley Lab and the University of Wisconsin-Milwaukee have reported the first full color infrared tomography. (Image by Cait Youngquist)
An iconic moment in the history of Hollywood movie magic was born in the 1939 film The Wizard of Oz when Judy Garland as Dorothy Gale stepped out of the black and white world of Kansas into the rainbow colored world of Oz. An iconic moment in the history of infrared imaging may have been born with the announcement of the first technique to offer full color IR tomography.
A collaboration between researchers at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of Wisconsin-Milwaukee (UWM) has combined Fourier Transform Infrared (FTIR) spectroscopy with computed tomography (CT-scans) to create a non-destructive 3D imaging technique that provides molecular-level chemical information of unprecedented detail on biological and other specimens with no need to stain or alter the specimen.
“The notion of having the colors in a 3D reconstructed image being tied to real chemistry is powerful,” says Michael Martin, an infrared imaging expert at Berkeley Lab’s Advanced Light Source, a DOE national user facility. “We’ve all seen pretty 3D renderings of medical scans with colors, for example bone-colored bones, but that’s simply an artistic choice. Now we can spectrally identify the specific types of minerals within a piece of bone and assign a color to each type within the 3D reconstructed image.”
Michael Martin at Berkeley Lab’s Advanced Light Source (Photo by Roy Kaltschmidt, Berkeley Lab)
Every individual type of molecule absorbs infrared (IR) light at specific wavelengths that are as characteristic as a human fingerprint. IR spectroscopy can be used to identify the chemical constituents of a sample and the application of the Fourier-transform algorithm allows all IR fingerprints to be simultaneously recorded. FTIR spectroscopy is especially valuable for imaging proteins and other biological samples because it is non-destructive and can be performed without altering the sample. Martin and Hirschmugl and their colleagues have combined FTIR with computed tomography, the technique for reconstructing 3D images out of multiple cross-sectional slices, to achieve what is believed to be the first demonstration of FTIR spectro-microtomography.
Carol Hirschmugl at University of Wisconsin’s Synchrotron Radiation Center
“FTIR spectro-microtomography involves low-energy IR photons that do not affect living systems and do not require artificial labels, contrast agents or sectioning,” Hirschmugl says. “It greatly enhances the capabilities of both FTIR spectroscopy and CT by creating a full-color spectro-microtomogram in which each voxel contains a complete spectrum (millions of spectra per sample) that provides a wealth of information for advanced spectral segregation techniques such as clustering, neural networks and principal-component analysis.”
The success of FTIR spectro-microtomography was enabled by the speed with which 2D FTIR images can be obtained at the SRC’s Infrared Environmental Imaging (IRENI) beamline. The SRC is a synchrotron radiation facility that provides infrared, ultra violet, and soft X-ray light for scientific research. IRENI offers one the nation’s highest performance IR imaging beamlines through the use of unique focal plane array detectors.
“With capabilities such as those at IRENI, we can obtain hundreds of 2D spectral images as a sample is rotated,” Martin says. “For each wavelength, we can then reconstruct a full 3D representation of the sample via computed tomography algorithms.”
Martin, Hirschmugl and their colleagues developed a motorized sample mount that precisely rotates the sample while holding it at the focus of an IR microscope. Data collection of 2D spectral transmission images as a function of sample angle is automated, and the computed tomography algorithms allow full reconstructions for every wavelength measured that are then reassembled into a complete spectrum for every voxel.
“We’ve been able to do a lot of exciting science with 2D FTIR imaging at the diffraction limit using synchrotron infrared beamlines, and it’s very exciting to now be able to expand this to true 3D spectroscopic imaging,” Martin says. “While the most immediate applications will be in biomedical imaging, I think full color FTIR spectro-microtomography will also be applicable to imaging 3D structures in biofuels, plants, rocks, algae, soils, agriculture and possibly even studies of art history where different layers of paints could be revealed.”
Spectro-microtomographic images of a human hair show absorptions of protein (red) and phospholipid (blue-green). Center, the medulla is observed to have little protein. Bottom, the medulla has higher concentrations of phospholipids.
The Berkeley Lab and UWM researchers have already successfully applied FTIR spectro-microtomography to obtain 3D images of the molecular architecture of the cell walls in a flowering plant – zinnia – and in a woody plant – poplar. A better understanding of the chemical composition and architecture of plant cell walls is critical to the ultimate success of making biofuels from plant biomass. The collaboration also applied FTIR spectro-microtomography to study human hair, which has a distinctive biochemical construction, and an intact grouping of pluripotent mouse stem cells.
“The hair study showed that spectral reconstructions can be done on larger fully hydrated biological samples and that we can spectrally identify a fully buried portion of the sample,” Hirschmugl says. “The mouse study shows that our technique has promise not only for stem cell screening without the use of dyes or probes, but also for promoting a better understanding of the biochemical structure of differentiating stem cells in their microenvironment.”
The collaborators are continuing to improve the efficiency by which they can collect and analyze FTIR spectro-microtomography with new advances being incorporated at IRENI and at IR beamline 5.4 of Berkeley Lab’s Advanced Light Source (ALS), a project being overseen by Martin. The work at the ALS is being done in collaboration with Berkeley Lab’s National Energy Research Scientific Computing Center (NERSC).
Other co-authors of the Nature Methods paper are Charlotte Dabat-Blondeau, Miriam Unger, Julia Sedlmair, Dilworth Parkinson, Hans Bechtel, Barbara Illman, Jonathan Castro, Marco Keiluweit, David Buschke, Brenda Ogle and Michael Nasse.
This research was funded by the DOE Office of Science and the National Science Foundation. Berkeley Lab’s ALS and NERSC are funded by the DOE Office of Science.
Berkeley Lab Study Reveals Origins of an Exotic Phase of Matter
Understanding superconductivity – whereby certain materials can conduct electricity without any loss of energy – has proved to be one of the most persistent problems in modern physics. Scientists have struggled for decades to develop a cohesive theory of superconductivity, largely spurred by the game-changing prospect of creating a superconductor that works at room temperature, but it has proved to be a tremendous tangle of complex physics.
Now scientists at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have teased out another important tangle from this giant ball of string, bringing us a significant step closer to understanding how high- temperature superconductors work their magic. Working with a model compound, the team illuminated the origins of the so-called “stripe phase” in which electrons become concentrated in stripes throughout a material, and which appears to be linked to superconductivity.
Ultrafast changes in the optical properties of strontium-doped lanthanum nickelate throughout the infrared spectrum expose a rapid dynamics of electronic localization in the nickel-oxide plane, shown at left. This process, illustrated on the right, comprises the first step in the formation of ordered charge patterns or “stripes.”
“We’re trying to understand nanoscale order and how that determines material properties such as superconductivity,” said Robert Kaindl, a physicist in Berkeley Lab’s Materials Sciences Division. “Using ultrafast optical techniques, we are able to observe how charge stripes start to form on a time scale of hundreds of femtoseconds.” A femtosecond is just one millionth of one billionth of a second.
Electrons in a solid material interact extremely quickly and on very short length scales, so to observe their behavior researchers have built extraordinarily powerful “microscopes” that zoom into fast events using short flashes of laser light. Kaindl and his team brought to bear the power of their ultrafast-optics expertise to understand the stripe phase in strontium-doped lanthanum nickelate (LSNO), a close cousin of high-temperature superconducting materials.
“We chose to work with LSNO because it has essential similarities to the cuprates (an important class of high-temperature superconductors), but its lack of superconductivity lets us focus on understanding just the stripe phase,” said Giacomo Coslovich, a postdoctoral researcher at Berkeley Lab working with Kaindl.
“With science, you have to simplify your problems,” Coslovich continued. “If you try to solve them all at once with their complicated interplay, you will never understand what’s going on.”
Giacomo Coslovich (left) and Robert Kaindl (right) next to the laser setup that generates extremely short pulses of light at “mid-infrared” wavelengths, far beyond the spectrum perceptible by the human eye.
Kaindl and Coslovich are corresponding authors on a paper reporting these results inNature Communications, titled, “Ultrafast charge localization in a stripe-phase nickelate.” Coauthoring the paper are Bernhard Huber, Yi Zhu, Yi-De Chuang, Zahid Hussain, Hans Bechtel, Michael Martin and Robert Schoenlein of Berkeley Lab, along with Wei-Sheng Lee, and Zhi-Xun Shen of SLAC National Accelerator Laboratory, and Takao Sasagawa of Tokyo Institute of Technology.
Stripes are seen in all high-temperature superconductors near the superconducting transition temperature. In this LSNO crystal stripes form only at cryogenic temperatures of about ‑168 degrees Celsius (approximately ‑271 °F), yet at far higher temperatures the team hit upon large changes of the material’s infrared reflectivity. These invisible “color” changes represent an energy threshold for electrical currents, dubbed the energetic “pseudogap”, which grows as the crystal cools – revealing a progressive localization of charges around the nickel atoms.
The scientists then examined the dynamics of LSNO in “pump-probe” experiments, where they melted stripes with an initial ultrafast pulse of laser light and measured the optical changes with a second, delayed pulse. This allowed them to map out the early steps of charge ordering, exposing surprisingly fast localization dynamics preceding the development of organized stripe patterns. A final twist came when they probed the vibrations between nickel and oxygen atoms, uncovering a remarkably strong coupling to the localized electrons with synchronous dynamics.
Beyond the ultrafast measurements, the team also studied X-ray scattering and the infrared reflectance of the material at the neighboring Advanced Light Source, to develop a thorough, cohesive understanding of the stripe phase and why it forms.
Said Kaindl, “We took advantage of our fortunate location in the national lab environment, where we have both these ultrafast techniques and the Advanced Light Source. This collaborative effort made this work possible.”
Having illuminated the origins of the stripe phase in LSNO, the researchers expect their results to provide new impetus to understanding the “pseudogap” in other correlated oxides – especially in high-temperature superconductors where fluctuating stripes occur while their role for the superconductivity mechanism remains unclear.
This research was supported by the U.S. Department of Energy, Office of Science.
Berkeley Lab Researchers Discover Universal Law for Light Absorption in 2D Semiconductors
(From left) Eli Yablonovitch, Ali Javey and Hui Fang discovered a simple law of light absorption for 2D semiconductors that should open doors to exotic new optoelectronic and photonic technologies. (Photo by Roy Kaltschmidt)
From solar cells to optoelectronic sensors to lasers and imaging devices, many of today’s semiconductor technologies hinge upon the absorption of light. Absorption is especially critical for nano-sized structures at the interface between two energy barriers called quantum wells, in which the movement of charge carriers is confined to two-dimensions. Now, for the first time, a simple law of light absorption for 2D semiconductors has been demonstrated.
Working with ultrathin membranes of the semiconductor indium arsenide, a team of researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) has discovered a quantum unit of photon absorption, which they have dubbed “AQ,” that should be general to all 2D semiconductors, including compound semiconductors of the III-V family that are favored for solar films and optoelectronic devices. This discovery not only provides new insight into the optical properties of 2D semiconductors and quantum wells, it should also open doors to exotic new optoelectronic and photonic technologies.
“We used free-standing indium arsenide membranes down to three nanometers in thickness as a model material system to accurately probe the absorption properties of 2D semiconductors as a function of membrane thickness and electron band structure,” says Ali Javey, a faculty scientist in Berkeley Lab’s Materials Sciences Division and a professor of electrical engineering and computer science at the University of California (UC) Berkeley. “We discovered that the magnitude of step-wise absorptance in these materials is independent of thickness and band structure details.”
Indium arsenide is a III–V semiconductor with electron mobility and velocity that make it an outstanding candidate for future high-speed, low-power opto-electronic devices.
Javey is one of two corresponding authors of a paper describing this research in the Proceedings of the National Academy of Sciences (PNAS). The paper is titled “Quantum of optical absorption in two-dimensional semiconductors.” Eli Yablonovitch, an electrical engineer who also holds joint appointments with Berkeley Lab and UC Berkeley, is the other corresponding author. Co-authors are Hui Fang, Hans Bechtel, Elena Plis, Michael Martin and Sanjay Krishna.
Previous work has shown that graphene, a two-dimensional sheet of carbon, has a universal value of light absorption. Javey, Yablonovitch and their colleagues have now found that a similar generalized law applies to all 2D semiconductors. This discovery was made possible by a unique process that Javey and his research group developed in which thin films of indium arsenide are transferred onto an optically transparent substrate, in this case calcium fluoride.
“This provided us with ultrathin membranes of indium arsenide, only a few unit cells in thickness, that absorb light on a substrate that absorbed no light,” Javey says. “We were then able to investigate the optical absorption properties of membranes that ranged in thickness from three to 19 nanometers as a function of band structure and thickness.”
In this FTIR microspectroscopy study, light absorption spectra are obtained from measured transmission and reflection spectra in which the incident light angle is perpendicular to the membrane.
Using the Fourier transform infrared spectroscopy (FTIR) capabilities of Beamline 1.4.3 at Berkeley Lab’s Advanced Light Source, a DOE national user facility, Javey, Yablonovitch and their co-authors measured the magnitude of light absorptance in the transition from one electronic band to the next at room temperature. They observed a discrete stepwise increase at each transition from indium arsenide membranes with an AQ value of approximately 1.7-percent per step.
“This absorption law appears to be universal for all 2D semiconductor systems,” says Yablonovitch. “Our results add to the basic understanding of electron–photon interactions under strong quantum confinement and provide a unique insight toward the use of 2D semiconductors for novel photonic and optoelectronic applications.”
This research was supported by DOE’s Office of Science and the National Science Foundation.
Of Aging Bones and Sunshine
Study at Berkeley Lab’s Advanced Light Source Links Vitamin D Deficiency to Accelerated Aging of Bones
Everyone knows that as we grow older our bones become more fragile. Now a team of U.S. and German scientists led by researchers with the U.S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley has shown that this bone-aging process can be significantly accelerated through deficiency of vitamin D – the sunshine vitamin.
Vitamin D deficiency is a widespread medical condition that has been linked to the health and fracture risk of human bone on the basis of low calcium intake and reduced bone density. However, working at Berkeley Lab’s Advanced Light ALS), a DOE national user facility, the international team demonstrated that vitamin D deficiency also reduces bone quality.
“The assumption has been that the main problem with vitamin D deficiency is reduced mineralization for the creation of new bone mass, but we’ve shown that low levels of vitamin D also induces premature aging of existing bone,” says Robert Ritchie, who led the U.S. portion of this collaboration. Ritchie holds joint appointments with Berkeley Lab’s Materials Sciences Division and the University of California (UC) Berkeley’s Materials Science and Engineering Department.
“Unraveling the complexity of human bone structure may provide some insight into more effective ways to prevent or treat fractures in patients with vitamin D deficiency,” says Björn Busse, of the Department of Osteology and Biomechanics at the University Medical Center in Hamburg, Germany, who led the German portion of the team.
Ritchie and Busse have reported their findings in the journal Science Translational Medicine. The paper is titled “Vitamin D Deficiency Induces Early Signs of Aging in Human Bone, Increasing the Risk of Fracture.” Co-authors also include Hrishikesh Bale, Elizabeth Zimmermann, Brian Panganiban, Holly Barth, Alessandra Carriero, Eik Vettorazzi, Josef Zustin, Michael Hahn, Joel Ager, Klaus Püschel and Michael Amling.