CLICK HERE TO READ ON IGB WEBSITE A tiny but prolific world of microbes encompasses everything around us, both inside and out. Microbiomes, which are comprised of diverse communities of microbes, play a pivotal role in shaping human health, yet the intricacies of how different microbial compositions influence our well-being remains largely unknown. In a recent study published in PNAS, researchers at the University of Illinois Urbana-Champaign describe a new framework they have created to predict how species within microbiomes interact with each other to create unique compositions. “Microbes can be used in medicine, aka ‘bugs as drugs’, and these microbial therapeutics hold the possibility of being the answer to many of the diseases we face today,” said Shreya Arya, a graduate student in the O’Dwyer lab. “We’re trying to get away from using antibiotics to solve these issues because over time bacteria have developed antibiotic resistance. If the gut gets infected because of a pathogen, we want a way to be able to change the composition of the gut microbiome so that the gut microbiome is restored to a healthy state and the pathogen’s abundance is suppressed.”
Unfortunately, assessing interactions between each microbe species across diverse environments would demand an exponential volume of experimental data that would not be feasible to model. To overcome this hurdle, James O’Dwyer (CAIM), an associate professor of plant biology, along with Arya and Ashish George, a former postdoctoral researcher in O’Dwyer’s lab, sought to create a model that could predict outcomes of microbial communities based on the microbes initially present at the start. The model would provide a “landscape interaction value” between every microbe, that essentially characterizes how much effect each of the microbes has on another’s abundance and the microbiome’s outcome. “When doing this modeling, it’s important to ask the right question,” said O’Dwyer. “We could exhaustively try to model all of the pairwise comparisons and higher order interactions between species, which would give us the full dynamics of how the community changes over time, but that would literally take forever. Instead, we asked, at the end of all these microbial interactions, who's still there? How abundant are they and then what are their functions in that end-point community?” To address these questions, the research team started with a computational model capable of simulating microbial communities and predicting their outcomes. In this process, they uncovered a surprising revelation — most of the landscape interactions between microbes were near zero. This means that most microbes had a minimal impact on the final outcome of the microbiome, with only a select few playing a crucial role in predicting these outcomes. The researchers then used a method from the field of signal detection, called compressive sensing, which allows more information to be extracted from datasets with a sparse representation. The model was trained using existing microbiome datasets, and the results of these interactions were verified through real-world experiments with the same microbiomes to see if the resulting interactions and composition matched the predictions. Intriguingly, the researchers found that the “sparsity”, or abundance of zeros, of the landscape interactions held true, both in the model and in the real-world experiments. “I think there’s a lot we can learn about ecological communities in general from this,” O’Dwyer said. “We often think there's all these complex interactions, and this leads the structure and community functions to be hard to predict. But this shows that sometimes the outcomes are a bit simpler than you might expect. The magic here is that you don't have to learn everything about every initial condition through to every final state. You just have to learn a bit of it and it can give you enough information to know the whole thing.” The team is now interested in exploring why so many microbial landscape interactions were near zero, and trying larger datasets to see if that changes the patterns they found. “We want to understand why this sparsity is present in the first place, if that can tell us something about how microbiomes fundamentally are assembled, and how those species interact with each other,” explained Arya. “For example, even though a soil microbiome has very different species taxonomically speaking compared to the human gut, there may be similarities in the ways that microbial species interact with each other that we can predict based on the environment.” Arya hopes to continue fine-tuning the model so that it can be used to study particular microbiomes of interest, and accommodate more diverse datasets. One ultimate goal is to be able to use the model in personalized medicine, to help predict whether patients are at risk of certain pathogens establishing within their microbiomes compared to others.“In order to create microbial therapeutics, we need to understand which microbial species we need to combine in which environments in order to get the best function. And this is a first step towards that goal,” said Arya. This work was funded by the Simons Foundation, and can be found at https://doi.org/10.1073/pnas.2307313120
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The new advance will enable pocket-sized devices that can perform detailed GPS-free precision navigation, medical imaging, food safety inspection and more. NEW YORK, NOVEMBER 9, 2023 — Lasers are essential tools for observing, detecting, and measuring things in the natural world that we can’t see with the naked eye. But the ability to perform these tasks is often restricted by the need to use expensive and large instruments. In a newly published cover-story paper in the journal Science, researcher Qiushi Guo demonstrates a novel approach for creating high-performance ultrafast lasers on nanophotonic chips. His work centers on miniaturizing mode-lock lasers — a unique laser that emits a train of ultrashort, coherent light pulses in femtosecond intervals, which is an astonishing quadrillionth of a second. Ultrafast mode-locked lasers are indispensable to unlocking the secrets of the fastest timescales in nature, such as the making or breaking of molecular bonds during chemical reactions, or light propagation in a turbulent medium. The high-speed, pulse-peak intensity and broad-spectrum coverage of mode-locked lasers have also enabled numerous photonics technologies, including optical atomic clocks, biological imaging, and computers that use light to calculate and process data. Unfortunately, state-of-the-art mode-locked lasers are currently expensive, power-demanding tabletop systems that are limited to laboratory use. “Our goal is to revolutionize the field of ultrafast photonics by transforming large lab-based systems into chip-sized ones that can be mass produced and field deployed,” said Guo, a faculty member with the CUNY Advance Science Research Center’s Photonics Initiative and a physics professor at the CUNY Graduate Center. “Not only do we want to make things smaller, but we also want to ensure that these ultrafast chip-sized lasers deliver satisfactory performances. For example, we need enough pulse-peak intensity, preferably over 1 Watt, to create meaningful chip-scale systems.” Realizing an effective mode-locked laser on a chip is not a straightforward process, however. Guo’s research leverages an emerging material platform known as thin-film lithium niobate (TFLN). This material enables very efficient shaping and precise control of laser pulses by applying an external radio frequency electrical signal. In their experiments, Guo’s team uniquely combined the high laser gain of III-V semiconductors and the efficient pulse shaping capability of TFLN nanoscale photonic waveguides to demonstrate a laser that can emit a high output peak power of 0.5 Watt. Beyond its compact size, the demonstrated mode-locked laser also exhibits many intriguing properties that are beyond reach by conventional ones, offering profound implications for future applications. For example, by adjusting the pump current of the laser, Guo was able to precisely tune the repetition frequencies of out pulses in a very wide range of 200 MHz. By employing the strong reconfigurability of the demonstrated laser, the research team hopes to enable chip-scale, frequency-stabilized comb sources, which are vital for precision sensing. Guo’s team will need to address additional challenges to realize scalable, integrated, ultrafast photonic systems that can be translated for use in portable and handheld devices, but his lab has overcome a major obstacle with this current demonstration. “This achievement paves the way for eventually using cell phones to diagnose eye diseases or analyzing food and environments for things like E. coli and dangerous viruses,” Guo said. “It could also enable futuristic chip-scale atomic clocks, which allows navigation when GPS is compromised or unavailable.” More information, including a copy of the paper, can be found online at the Science press package at https://www.eurekalert.org/press/scipak/ Bartering Light for Light: Scientists Discover New System to Control the Chaotic Behavior of Light11/2/2023 CLICK HERE TO READ ON CUNY WEBSITE
Studying how light beams interfere with each other in a stadium shaped arena gives researchers insight on its complex behavior. NEW YORK, November 2, 2023 -- Harnessing and controlling light is vital for the development of technology, including energy harvesting, computation, communications, and biomedical sensing. Yet, in real-world scenarios, complexity in light’s behavior poses challenges for its efficient control. Physicist Andrea Alù likens the behavior of light in chaotic systems to the initial break shot in a game of billiards. “In billiards, tiny variations in the way you launch the cue ball will lead to different patterns of the balls bouncing around the table,” said Alù, Einstein Professor of Physics at the CUNY Graduate Center, founding director of the Photonics Initiative at the CUNY Advanced Science Research Center and distinguished professor at CUNY. “Light rays operate in a similar way in a chaotic cavity. It becomes difficult to model to predict what will happen because you could run an experiment many times with similar settings, and you’ll get a different response every time.” In a new study published in Nature Physics, a team led by researchers at CUNY describe a new platform for controlling the chaotic behavior of light by tailoring its scattering patterns using light itself. The project was led by co-first authors Xuefeng Jiang, a former postdoctoral researcher in Alù’s lab who is now assistant professor of Physics with Seton Hall University, and Shixiong Yin, a graduate student in Alù’s lab. Conventional platforms for studying light’s behaviors typically use circular or regularly shaped resonant cavities in which light bounces and scatters in more predictable patterns. In a circular cavity, for example, only predictable and distinct frequencies (colors of light) survive, and each supported frequency is associated with a specific spatial pattern, or mode. One mode at a single frequency is sufficient to understand the physics at play in a circular cavity, but this approach does not unleash the full complexity of light behaviors seen in complex platforms, Jaing said. “In a cavity that supports chaotic patterns of light, any single frequency injected into the cavity can excite thousands of light patterns, which is conventionally thought to doom the chances of controlling the optical response,” Jaing said. “We have demonstrated that it is possible to control this chaotic behavior.” To address the challenge, the team designed a large stadium-shaped cavity with an open top and two channels on opposing sides that direct light into the cavity. As incoming light scatters off the walls and bounces around, a camera above records the amount of light escaping the stadium and its spatial patterns. The device features knobs on its sides to manage the light intensity at the two inputs, and the delay between them. Opposing channels cause the light beams to interfere with each other in the stadium cavity, enabling the control of one beam’s scattering by the other through a process known as coherent control—essentially, using light to control light, according to Alù. By adjusting the relative intensity and delay of the light beams entering the two channels, remarkably, researchers consistently altered the light’s radiation pattern outside the cavity. This control was enabled through a rare behavior of light in resonant cavities, called “reflectionless scattering modes” (RSMs), which had been theoretically predicted before but not observed in optical cavity systems. According to Yin, the ability to manipulate RSMs demonstrated in this work allows for the efficient excitation and control of complex optical systems, which has implications for energy storage, computing, and signal processing. “We found at certain frequencies our system can support two independen, overlapping RSMs, which cause all of the light to enter the stadium cavity without reflections back to our channel ports, thus enabling its control,” said Yin. “Our demonstration deals with optical signals within the bandwidth of optical fibers that we use in our daily life, so this finding paves a new way for better storage, routing, and control of light signals in complex optical platforms.” The researchers aim to incorporate additional knobs in future studies, offering more degrees of freedom to unravel further complexities in the behavior of light. “Coherent Control of Chaotic Optical Microcavity with Reflectionless Scattering Modes,” by Xuefeng Jiang, Shixiong Yin, Huanan Li, Jiamin Quan, Heedong Goh, Michele Cotrufo, Julius Kullig, Jan Wiersig, and Andrea Alù. |