Rice University’s new light-amplifying nanoparticle consists of a 190-nanometer diameter sphere of barium tin oxide surrounded by a 30-nanometer thick shell of gold. (Image by Yu Zhang /Rice University).Rice University photonics researchers have unveiled a new nanoparticle amplifier that can generate infrared light and boost the output of one light by capturing and converting energy from a second light.
The innovation, the latest from Rice's Laboratory for Nanophotonics (LANP), is described online in a paper in the American Chemical Society journal Nano Letters. The device functions much like a laser, but while lasers have a fixed output frequency, the output from Rice's nanoscale "optical parametric amplifier" (OPA) can be tuned over a range of frequencies that includes a portion of the infrared spectrum.
"Tunable infrared OPA light sources today cost around a $100,000 and take up a good bit of space on a tabletop or lab bench," said study lead author Yu Zhang, a former Rice graduate student at LANP. "What we've demonstrated, in principle, is a single nanoparticle that serves the same function and is about 400 nanometers in diameter."
By comparison, that's about 15 times smaller than a red blood cell, and Zhang said shrinking an infrared light source to such a small scale could open doors to new kinds of chemical sensing and molecular imaging that aren't possible with today's state-of-the-art nanoscale infrared spectroscopy.
Walking uphill as an enzyme (chorismate mutase shown in purple) changes conformation, it moves to a region of the catalytic landscape where its substrate (chorismate in aqua and red) can overcome the energy barrier and reach the transition state. (Credit: Warshel/Bora)Enzymes play a crucial role in most biological processes—controlling energy transduction, as well as the transcription and translation of genetic information and signaling. They possess a remarkable capacity to accelerate biochemical reactions by many orders of magnitude compared to their uncatalyzed counterparts.
So there is broad scientific interest in understanding the origin of the catalytic power of enzymes on a molecular level. While many hypotheses have been put forward using both experimental and computational approaches, they must be examined critically.
In The Journal of Chemical Physics, a group of University of Southern California (USC) researchers present a critical review of the dynamical concept—time-dependent coupling between protein conformational motions and chemical reactions—that explores all reasonable definitions of what does and does not qualify as a dynamical effect.
The group's work centers on multiscale computer simulations—for which Arieh Warshel, currently a distinguished professor of chemistry at USC, was awarded the 2013 Nobel Prize in chemistry, along with Michael Levitt and Martin Karplus—for exploring the complex actions of enzymes.
"Our study reviews various proposals governing the catalytic efficiency of enzymes, which requires constructing free energy surfaces associated with the chemical reactions, as well as catalytic landscapes comprising conformational and chemical coordinates," explained Ram Prasad Bora, co-author and a postdoctoral assistant working with Warshel. "It's far from trivial to construct these surfaces using reliable theoretical approaches."
For the group's studies, they tend to construct catalytic free energy surfaces by combining an empirical valence bond (EVB) approach, developed by Warshel and colleagues in the early 1980s to determine reaction free energies of enzymatic reactions, with corresponding uncatalyzed solution reaction surfaces constructed via computational "ab initio quantum chemical calculations." But the "quality of EVB free energy surfaces are improved further—to a desired quantum chemical level—by using a paradynamics approach," Bora added.
Comparing the free energy surfaces—and the various factors contributing to these surfaces—for both enzymatic and solution reactions enabled the group to identify the factors contributing to enzyme catalysis.
"In our studies, it's electrostatic free energy," said Bora. "But, to specifically address dynamical and kinetic isotope effects, we used an autocorrelation function of the energy gap, catalytic landscapes—constructed using a renormalization approach—and a quantum classical patch (QCP) approach to determine that dynamics don't contribute to the catalytic power of enzymes."
The key significance of the group's work? "The catalytic activity of enzymes is fundamental to life, so gaining a solid understanding of the factors controlling and contributing to their activity at the molecular level is crucial," said Bora.
With high-quality scientific data now available for the most interesting and complex biological molecules, "it's essential to re-examine various catalytic proposals—especially electrostatic- and dynamic-based proposals," he continued. "Our review focuses on clarifying the role of logical definitions of different catalytic proposals, as well as on the need for a clear formulation in terms of the assumed potential surface and reaction coordinates."
The group determined, in previous efforts, that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes. Their current work focuses on exploring the alternative dynamical proposal.
In terms of applications, the group's enzyme modeling offers "major medical and fundamental value," said Warshel. "For example, it can provide big improvements in enzyme design and advances in drug resistance. Most significant to me, personally, is that it's a solution to the 100-year-old puzzle of how enzymes really do and don't work."
The scientific field of "computational enzyme designing," in particular, stands to benefit from the group's work. "The idea is to tailor desired enzymes for specific purposes—to be used as catalysts for several chemical and biochemical processes at industrial scales—using computational approaches to create artificial enzymes, which can be tested and further improved in laboratories later," explained Bora.
While the concept of designing enzymes computationally from scratch was initially considered intriguing, the field is evolving slowly. "This is largely because the current enzyme designing protocols don't take the actual enzyme catalytic factors into account," Bora continued. "Our work presents a very detailed discussion of these factors, and clarifies that it isn't useful to try to optimize dynamical effects in enzyme design. Focusing on other factors will enable devising future designing protocols on a scientific basis—which will increase the success rate of computationally designed enzymes."
What's next for the group? "More efforts in enzyme design and drug resistance, as well as studies of complex molecular motors and signal transduction," said Warshel.
The group's critical analysis work will help further the exploration of the catalytic factors controlling enzyme catalysis. "Our clear vision about the enzyme catalytic factors means we can now devise effective artificial enzyme design protocols—purely on a scientific basis—that may fill the gap between rational design and laboratory discovery. This can provide insights into another fundamental issue in biology: What controls the evolution of proteins and enzymes?" noted Bora. "Successful design of enzymes may also help in the control of metabolic pathways."
Combining the results from radiative and non-radiative relaxation processes enabled a complete picture of the filled and unfilled energy levels to be obtained. Source: HZB/R. GolnakThe team demonstrated how a detailed picture of theelectronic states can be ascertained by systematically comparing all of the interactive electronic processes in a simple system of aqueous iron(II). The results have now been published in Scientific Reports, the open access journal from Nature Group publishing.
If a blindman feels the leg of an elephant, he can conclude something about the animal. And perhaps the conclusion would be that an elephant is constructed like a column. That is not incorrect, but not the whole story either. So it is with measurement techniques: they show a particular aspect very well, yet others not at all. Now an HZB Institute of Methods for Material Development team headed by Professor Emad Aziz has succeeded in combining two different methods in such a way that a practically complete picture of the electronic states and interactions of a molecule in an aqueous solution results.
Flick a switch on a dark winter day and your office is flooded with bright light, one of many everyday miracles to which we are all usually oblivious.
A physicist would probably describe what is happening in terms of the particle nature of light. An atom or molecule in the fluorescent tube that is in an excited state spontaneously decays to a lower energy state, releasing a particle called a photon. When the photon enters your eye, something similar happens but in reverse. The photon is absorbed by a molecule in the retina and its energy kicks that molecule into an excited state.
Light is both a particle and a wave, and this duality is fundamental to the physics that rule the Lilliputian world of atoms and molecules. Yet it would seem that in this case the wave nature of light can be safely ignored.
Kater Murch, assistant professor of physics in Arts & Sciences at Washington University in St. Louis, might give you an argument about that. His lab is one of the first in the world to look at spontaneous emission with an instrument sensitive to the wave rather than the particle nature of light, work described in the May 20th issue of Nature Communications.
A new subcommittee is meant to monitor advances and milestones in A.I., including in the federal realm, the private sector, and internationally.Get ready because artificial intelligence is on the White House’s radar, and it’s taking the field seriously.
The White House this week announced the new National Science and Technology Council (NSTC) Subcommittee on Machine Learning and Artificial Intelligence will meet for the first time next week, and the White House Office of Science and Technology Policy will cohost four workshops to create a dialogue around the positives and negatives of artificial intelligence and machine learning.
“Like any transformative technology … artificial intelligence carries some risk and presents complex policy challenges along several dimensions, from jobs and the economy to safety and regulatory questions,” Deputy U.S. Chief Technology Officer Ed Felten wrote. “For example, A.I. will create new jobs while phasing out some old ones—magnifying the importance of programs like TechHire that are preparing our workforce with the skills to get ahead in today’s economy, and tomorrow’s.”
The following workshops will be held over the next few months:
Dr. Azad Shademan and Ryan Decker during supervised autonomous in-vivo bowel anastomosis performed by the Smart Tissue Autonomous Robot. (Credit: Axel Krieger)While companies, such as Intuitive Surgical Inc., are utilizing robots in the operating room to assist with surgery, researchers from Johns Hopkins University and the Children’s National Health System have developed a robotic surgeon that recently performed a soft-tissue surgery with limited guidance from humans.
Called the Smart Tissue Automation Robot (STAR), the system “consists of tools for suturing as well as fluorescent and 3D imaging, force sensing, and submillimeter positioning,” the researchers wrote in their paper appearing in Science Translational Medicine.
Each year in the U.S., roughly 44.5 million soft-tissue surgeries are performed. With autonomous surgeries, medical practitioners will be able to provide substantial benefits through improved safety by pushing out the likelihood of human error, according to the researchers.
Interestingly, another study recently published in BMJ by Johns Hopkins University researchers suggests medical error may be the third leading cause of death in the country, claiming about 251,000 lives per year.
Under a surgeon’s supervision, the STAR system performed a procedure called anastomosis, where two tubular ends are connected with sutures. The procedure is performed more than 1 million times per year in the U.S., according to the researchers. Leakages occur nearly 20 percent of the time in colorectal surgery, and 25 to 30 percent of the time in abdominal surgery.
This illustration depicts an experiment at SLAC that revealed how a protein from photosynthetic bacteria changes shape in response to light in less than a trillionth of a second. (Credit: SLAC National Accelerator Laboratory)For the variety of Earth’s fauna and flora, sunlight provides nutrients essential for life.
“Converting light from the sun into energy is what keeps us alive,” Sébastien Boutet, a senior staff scientist at SLAC National Accelerator Laboratory’s Linac Coherent Light Source (LCLS), told R&D Magazine.
While scientists know biomolecules harness light to carry out important biological processes, it’s difficult to capture these reactions on the atomic and molecular levels because they occur so quickly.
Boutet, along with a team of international researchers, used the LCLS’ powerful x-ray laser to capture such a reaction at speeds hitherto unattainable.
“We’re trying to see ultrafast reactions” and “the x-ray source that we have here is very unique,” said Boutet, who took a job at LCLS about nine years ago to develop the beam line used in the experiment.
Flick a switch on a dark winter day and your office is flooded with bright light, one of many everyday miracles to which we are all usually oblivious.
