Tag Archives: Friedrich Schiller University Jena

Light-based neural networks

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It’s unusual to see the same headline used to highlight research from two different teams released in such proximity, February 2024 and July 2024, respectively. Both of these are neuromorphic (brainlike) computing stories.

February 2024: Neural networks made of light

The first team’s work is announced in a February 21, 2024 Friedrich Schiller University press release, Note: A link has been removed,

Researchers from the Leibniz Institute of Photonic Technology (Leibniz IPHT) and the Friedrich Schiller University in Jena, along with an international team, have developed a new technology that could significantly reduce the high energy demands of future AI systems. This innovation utilizes light for neuronal computing, inspired by the neural networks of the human brain. It promises not only more efficient data processing but also speeds many times faster than current methods, all while consuming considerably less energy. Published in the prestigious journal „Advanced Science,“ their work introduces new avenues for environmentally friendly AI applications, as well as advancements in computerless diagnostics and intelligent microscopy.

Artificial intelligence (AI) is pivotal in advancing biotechnology and medical procedures, ranging from cancer diagnostics to the creation of new antibiotics. However, the ecological footprint of large-scale AI systems is substantial. For instance, training extensive language models like ChatGPT-3 requires several gigawatt-hours of energy—enough to power an average nuclear power plant at full capacity for several hours.

Prof. Mario Chemnitz, new Junior Professor of Intelligent Photonic SystemsExternal link at Friedrich Schiller University Jena, and Dr Bennet Fischer from Leibniz IPHT in Jena, in collaboration with their international team, have devised an innovative method to develop potentially energy-efficient computing systems that forego the need for extensive electronic infrastructure. They harness the unique interactions of light waves within optical fibers to forge an advanced artificial learning system.

A single fiber instead of thousands of components

Unlike traditional systems that rely on computer chips containing thousands of electronic components, their system uses a single optical fiber. This fiber is capable of performing the tasks of various neural networks—at the speed of light. “We utilize a single optical fiber to mimic the computational power of numerous neural networks,“ Mario Chemnitz, who is also leader of the “Smart Photonics“ junior research group at Leibniz IPHT, explains. “By leveraging the unique physical properties of light, this system will enable the rapid and efficient processing of vast amounts of data in the future.“

Delving into the mechanics reveals how information transmission occurs through the mixing of light frequencies: Data—whether pixel values from images or frequency components of an audio track—are encoded onto the color channels of ultrashort light pulses. These pulses carry the information through the fiber, undergoing various combinations, amplifications, or attenuations. The emergence of new color combinations at the fiber’s output enables the prediction of data types or contexts. For example, specific color channels can indicate visible objects in images or signs of illness in a voice.

A prime example of machine learning is identifying different numbers from thousands of handwritten characters. Mario Chemnitz, Bennet Fischer, and their colleagues from the Institut National de la Recherche Scientifique (INRS) in Québec utilized their technique to encode images of handwritten digits onto light signals and classify them via the optical fiber. The alteration in color composition at the fiber’s end forms a unique color spectrum—a „fingerprint“ for each digit. Following training, the system can analyze and recognize new handwriting digits with significantly reduced energy consumption.

System recognizes COVID-19 from voice samples

“In simpler terms, pixel values are converted into varying intensities of primary colors—more red or less blue, for instance,“ Mario Chemnitz details. “Within the fiber, these primary colors blend to create the full spectrum of the rainbow. The shade of our mixed purple, for example, reveals much about the data processed by our system.“

The team has also successfully applied this method in a pilot study to diagnose COVID-19 infections using voice samples, achieving a detection rate that surpasses the best digital systems to date.

“We are the first to demonstrate that such a vibrant interplay of light waves in optical fibers can directly classify complex information without any additional intelligent software,“ Mario Chemnitz states.

Since December 2023, Mario Chemnitz has held the position of Junior Professor of Intelligent Photonic Systems at Friedrich Schiller University Jena. Following his return from INRS in Canada in 2022, where he served as a postdoc, Chemnitz has been leading an international team at Leibniz IPHT in Jena. With Nexus funding support from the Carl Zeiss Foundation, their research focuses on exploring the potentials of non-linear optics. Their goal is to develop computer-free intelligent sensor systems and microscopes, as well as techniques for green computing.

Here’s a link to and a citation for the paper,

Neuromorphic Computing via Fission-based Broadband Frequency Generation by Bennet Fischer, Mario Chemnitz, Yi Zhu, Nicolas Perron, Piotr Roztocki, Benjamin MacLellan, Luigi Di Lauro, A. Aadhi, Cristina Rimoldi, Tiago H. Falk, Roberto Morandotti. Advanced Science Volume 10, Issue 35 December 15, 2023 2303835 DOI: https://doi.org/10.1002/advs.202303835. First published: 02 October 2023

This paper is open access.

July 2024: Neural networks made of light

A July 12, 2024 news item on ScienceDaily announces research from another German team,

Scientists propose a new way of implementing a neural network with an optical system which could make machine learning more sustainable in the future. The researchers at the Max Planck Institute for the Science of Light have published their new method in Nature Physics, demonstrating a method much simpler than previous approaches.

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A July 12, 2024 Max Planck Institute for the Science of Light press release (also on EurekAlert), which originated the news item, provides more detail about their approach to neuromorphic computiing,

Machine learning and artificial intelligence are becoming increasingly widespread with applications ranging from computer vision to text generation, as demonstrated by ChatGPT. However, these complex tasks require increasingly complex neural networks; some with many billion parameters. This rapid growth of neural network size has put the technologies on an unsustainable path due to their exponentially growing energy consumption and training times. For instance, it is estimated that training GPT-3 consumed more than 1,000 MWh of energy, which amounts to the daily electrical energy consumption of a small town. This trend has created a need for faster, more energy- and cost-efficient alternatives, sparking the rapidly developing field of neuromorphic computing. The aim of this field is to replace the neural networks on our digital computers with physical neural networks. These are engineered to perform the required mathematical operations physically in a potentially faster and more energy-efficient way.

Optics and photonics are particularly promising platforms for neuromorphic computing since energy consumption can be kept to a minimum. Computations can be performed in parallel at very high speeds only limited by the speed of light. However, so far, there have been two significant challenges: Firstly, realizing the necessary complex mathematical computations requires high laser powers. Secondly, the lack of an efficient general training method for such physical neural networks.

Both challenges can be overcome with the new method proposed by Clara Wanjura and Florian Marquardt from the Max Planck Institute for the Science of Light in their new article in Nature Physics. “Normally, the data input is imprinted on the light field. However, in our new methods we propose to imprint the input by changing the light transmission,” explains Florian Marquardt, Director at the Institute. In this way, the input signal can be processed in an arbitrary fashion. This is true even though the light field itself behaves in the simplest way possible in which waves interfere without otherwise influencing each other. Therefore, their approach allows one to avoid complicated physical interactions to realize the required mathematical functions which would otherwise require high-power light fields. Evaluating and training this physical neural network would then become very straightforward: “It would really be as simple as sending light through the system and observing the transmitted light. This lets us evaluate the output of the network. At the same time, this allows one to measure all relevant information for the training”, says Clara Wanjura, the first author of the study. The authors demonstrated in simulations that their approach can be used to perform image classification tasks with the same accuracy as digital neural networks.

In the future, the authors are planning to collaborate with experimental groups to explore the implementation of their method. Since their proposal significantly relaxes the experimental requirements, it can be applied to many physically very different systems. This opens up new possibilities for neuromorphic devices allowing physical training over a broad range of platforms.

Here’s a link to and a citation for the paper,

Fully nonlinear neuromorphic computing with linear wave scattering by Clara C. Wanjura & Florian Marquardt. Nature Physics (2024) DOI: https://doi.org/10.1038/s41567-024-02534-9 Published: 09 July 2024

This paper is open access.

Keanu Reeves molecule: protector of plants?

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Courtesy: Wallpaperstopick [downloaded from https://wallpaperstopick.blogspot.com/2012/05/keanu-reeves.html]

The Keanu Reeves molecule is produced by bacteria.according to a February 6, 2023 news item on phys.org,

Bacteria of the genus Pseudomonas produce a strong antimicrobial natural product, as researchers at the Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI) have discovered. They proved that the substance is effective against both plant fungal diseases and human-pathogenic fungi. The study was published in the Journal of the American Chemical Society and highlighted in an editorial in Nature.

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A February 6, 2023 Leibniz Institute for Natural Product Research and Infection Biology – Hans Knoell Institute (Leibniz-HKI) press release (also on EurekAlert) by Charlotte Fuchs, which originated the news item, highlights both the published study and the special article in Nature magazine, Note: A link has been removed,

The newly discovered natural product group of keanumycins in bacteria works effectively against the plant pest Botrytis cinerea, which triggers grey mould rot and causes immense harvest losses every year. But the active ingredient also inhibits fungi that are dangerous to humans, such as Candida albicans. According to previous studies, it is harmless to plant and human cells.

Keanumycins could therefore be an environmentally friendly alternative to chemical pesticides, but they could also offer an alternative in the fight against resistant fungi. “We have a crisis in anti-infectives,” explains Sebastian Götze, first author of the study and postdoc at Leibniz-HKI. “Many human-pathogenic fungi are now resistant to antimycotics – partly because they are used in large quantities in agricultural fields.”

Deadly like Keanu Reeves

The fact that the researchers have now found a new active ingredient in bacteria of the genus Pseudomonas is no coincidence. “We have been working with pseudomonads for some time and know that many of these bacterial species are very toxic to amoebae, which feed on bacteria,” says study leader Pierre Stallforth. He is the head of the department of Paleobiotechnology at Leibniz-HKI and professor of Bioorganic Chemistry and Paleobiotechnology at Friedrich Schiller University in Jena. It appears that several toxins are responsible for the deadly effect of the bacteria, of which only one was known so far. In the genome of the bacteria, the researchers have now found biosynthesis genes for the newly discovered natural products, the keanumycins A, B and C. This group of natural products belongs to the nonribosomal lipopeptides with soap-like properties.

Together with colleagues at the Bio Pilot Plant of the Leibniz-HKI, the researchers succeeded in isolating one of the keanumycins and conducting further tests. “The lipopeptides kill so efficiently that we named them after Keanu Reeves because he, too, is extremely deadly in his roles,” Götze explains with a wink.

The researchers suspected that keanumycins could also kill fungi, as these resemble amoebas in certain characteristics. This assumption was confirmed together with the Research Centre for Horticultural Crops at the University of Applied Sciences Erfurt. There, Keanumycin was shown to be effective against grey mould rot on hydrangea leaves. In this case, culture fluid that no longer contained bacterial cells was sufficient to significantly inhibit the growth of the fungus.

“Theoretically, the keanumycin-containing supernatant from Pseudomonas cultures could be used directly for plants,” says Götze. Further testing will be carried out together with the colleagues in Erfurt. Keanumycin is biodegradable, so no permanent residues should form in the soil. This means that the natural product has the potential to become an environmentally friendly alternative to chemical pesticides.

Fungal diseases such as Botrytis cinerea, which causes grey mould rot, cause immense harvest losses in fruit and vegetable cultivation every year. More than 200 different types of fruit and vegetables are affected, especially strawberries and unripe grapes.

Possible applications in humans

“In addition, we tested the isolated substance against various fungi that infect humans. We found that it strongly inhibits the pathogenic fungus Candida albicans, among others,” says Götze.

Instead of plants, Keanumycin could therefore possibly also be used in humans. According to the tests conducted so far, the natural product is not highly toxic for human cells and is already effective against fungi in very low concentrations. This makes it a good candidate for the pharmaceutical development of new antimycotics. These are also urgently needed, as there are very few drugs against fungal infections on the market.

The work was supported by the Werner Siemens Foundation, the Leibniz Association and the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) as part of the Balance of the Microverse Cluster of Excellence, and funded by the Dr. Illing Foundation.

The study was highlighted by Nature in a “News & Views” article.

Here are citations and links to both the published study and the article in Nature,

Ecological Niche-Inspired Genome Mining Leads to the Discovery of Crop-Protecting Nonribosomal Lipopeptides Featuring a Transient Amino Acid Building Block by Sebastian Götze, Raghav Vij, Katja Burow, Nicola Thome, Lennart Urbat, Nicolas Schlosser, Sebastian Pflanze, Rita Müller, Veit G. Hänsch, Kevin Schlabach, Leila Fazlikhani, Grit Walther, Hans-Martin Dahse, Lars Regestein, Sascha Brunke, Bernhard Hube, Christian Hertweck, Philipp Franken, and Pierre Stallforth. J. Am. Chem. Soc. 2023, 145, 4, 2342–2353 DOI: https://doi.org/10.1021/jacs.2c11107 Publication Date:January 20, 2023 Copyright © 2023 The Authors. Published by American Chemical Society

and

Bacterial defence repurposed to fight blight (News and Views article) by Andrew Mitchinson. Nature 614, 39 (2023) DOI: https://doi.org/10.1038/d41586-023-00195-x Published: 30 January 2023

Both the study and the ‘News and Views’ article are behind a paywall.

German scientists battle tough mucus

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A December 15, 2017 news item on ScienceDaily highlights cystic fibrosis research being done in Germany,

Around one in 3,300 children in Germany is born with Mucoviscidosis [cystic fibrosis; CF]. A characteristic of this illness is that one channel albumen on the cell surface is disturbed by mutations. Thus, the amount of water of different secretions in the body is reduced which creates a tough mucus. As a consequence, inner organs malfunction. Moreover, the mucus blocks the airways. Thus, the self regulatory function of the lung is disturbed, the mucus is colonized by bacteria and chronic infections follow. The lung is so significantly damaged that patients often die or need to have a lung transplant. The average life expectancy of a patient today is around 40 years. This is due to medical progress. Permanent treatment with inhaled antibiotics play a considerable part in this. The treatment can’t avoid the colonization by bacteria completely but it can keep it in check for a longer period of time. However, the bacteria defend themselves with a development of resistance and with the growth of so-called biofilms underneath the layer of mucus, which mostly block off the bacteria in the lower rows like a protective shield.

A complex way to the Pathogens

Scientists of the Friedrich Schiller University Jena, Germany succeeded in developing a much more efficient method to treat the airway infections which are often lethal. Crucial are nanoparticles that transport the antibiotics more efficiently to their destination….

A December 15, 2017 Friedrich Schiller University Jena press release (also on EurekAlert), which originated the news item, expands on the theme,

“Typically, the drugs are applied by inhalation in the body. Then they make a complicated way through the body to the pathogens and many of them don’t make it to their destination,” states Prof. Dr Dagmar Fischer of the chair for Pharmaceutical Technology at the University of Jena, who supervised the project together with her colleague Prof. Dr Mathias Pletz, a pulmonologist and infectious diseases physician, from the Center for Infectious Diseases and Infection Control at the Jena University Hospital. The project was supported by the Deutsche Forschungsgemeinschaft. First of all, the active particles need to have a certain size to be able to reach the deeper airways and not to bounce off somewhere else before. Ultimately, they have to penetrate the thick layer of mucus on the airways as well as the lower layers of the bacteria biofilm.

Nanoparticles travel more efficiently

To overcome the strong defense, the researchers encapsulated the active agents, like the antibiotic Tobramycin, in a polyester polymer. Thus, they created a nanoparticle which they then tested in the laboratory where they beforehand had simulated the present lung situation, in a static as well as in a dynamic state, i. e. with simulated flow movements. Therefore Pletz’s research group had developed new test systems, which are able to mimick the situation of the chronically infected CF-lung. The scientists discovered that their nanoparticle travels more easily through the sponge-like net of the mucus layer and is finally able to kill off the pathogens without any problems. Moreover, an additionally applied coating of polyethylenglycol makes it nearly invisible for the immune system. “All materials of a nanocarrier are biocompatible, biodegradable, nontoxic and therefore not dangerous for humans,” the researcher informs.

However, the Jena scientists don’t know yet exactly why their nanoparticle fights the bacteria so much more efficiently. But they want to finally get clarification in the year ahead. “We have two assumptions: Either the much more efficient transport method advances significantly larger amounts of active ingredients to the center of infection, or the nanoparticle circumvents a defense mechanism, which the bacterium has developed against the antibiotic,” the Jena Pharmacist Fischer explains. “This would mean, that we succeeded in giving back its impact to an antibiotic, which had already lost it through a development of resistance of the bacteria.”

“More specifically, we assume that bacteria from the lower layers of the biofilm transform into dormant persisters and hardly absorb any substances from outside. In this stadium, they are tolerant to most antibiotics, which only kill off self-dividing bacteria. The nanoparticles transport the antibiotics more or less against their will to the inner part of the cell, where they can unfold their impact,” Mathias Pletz adds.

Additionally, the Jena research team had to prepare the nanoparticles for the inhalation. Because at 200 nanometers the particle is too small to get into the deeper airways. “The breathing system filters out particles that are too big as well as those which are too small,” Dagmar Fischer explains. “So, we are left with a preferred window of between one and five micrometers.” The Jena researchers also have promising ideas for resolving this problem.

Coating of Nanoparticles enhances the impact of Antibiotics against Biofilms

The scientists from Jena are at this point already convinced to have found a very promising method to fight respiratory infections of patients with mucoviscidosis. Thus they may be able to contribute to a higher life expectancy of those affected. “We were able to show that the nanoparticle coating improves the impact of the antibiotics against biofilm by a factor of 1,000,” the pulmonologist and infectious diseases physician is happy to say.

It’s exciting news and I wish the researchers great success. Perhaps, one day, they will publish a paper about their work.

Sweet, sugary computer (calculator); chemistry in action

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This computer is also described as sugar-based molecular computing in a June 19, 2014 news item on Nanowerk,

In a chemistry lab at the Friedrich Schiller University Jena (Germany): Prof. Dr. Alexander Schiller works at a rectangular plastic board with 384 small wells. The chemist carefully pipets some drops of sugar solution into a row of the tiny reaction vessels. As soon as the fluid has mixed with the contents of the vessels, fluorescence starts in some of the wells. What the Junior Professor for Photonic Materials does here – with his own hands – could also be called in a very simplified way, the ‘sweetest computer in the world’. The reason: the sugar molecules Schiller uses are part of a chemical sequence for information processing.

A June 19, 2014 Friedrich Schiller University Jena news release (also on EurekAlert), which originated the news item, provides an description by the lead researcher, Schiller,

Professor Schiller explains. “There is either electricity flowing between both poles of an electric conductor or there isn’t.” These potential differences are being coded as “0” and “1” and can be linked via logic gates – the Boolean operators like AND, OR, NOT. In this way, a number of different starting signals and complex circuits are possible.

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These logic links however can also be realized with the help of chemical substances, as the Jena chemists were able to show. For their ‘sugar computer’ they use several components: One fluorescent dye and a so-called fluorescence quencher. “If there are both components involved, the colorant can’t display its impact and we don’t see a fluorescence signal,” Schiller says. But if sugar molecules are involved, the fluorescence quencher reacts with the sugar and thus loses its capability to suppress the fluorescence signal, which makes the dye fluorescent. Depending on whether the dye, the fluorescence quencher and the sugar are on hand to give the signal, a fluorescent signal results – “1” – or no signal – “0”.

“We link chemical reactions with computer algorithms in our system in order to process complex information,” Martin Elstner explains. “If a fluorescence signal is registered, the algorithm determines what goes into the reaction vessel next.” In this way signals are not translated and processed in a current flow, like in a computer but in a flow of matter. That their chemical processing platform works, Schiller and his staff demonstrated in the current study with the sample calculation 10 + 15. “It took our sugar computer about 40 minutes, but the result was correct,” Prof. Schiller says smiling, and clarifies: “It is not our aim to develop a chemical competition to established computer chips.” The chemist rather sees the field of application in medical diagnostics. So it is for instance conceivable to connect the chemical analysis of several parameters of blood and urine samples via the molecular logic platform for a final diagnosis and thus enable decisions for therapies.

Here’s a link to and a citation for the paper,

Sugar-based Molecular Computing by Material Implication by Martin Elstner, Jörg Axthelm, and Prof.Dr. Alexander Schiller. Angewandte Chemie International Edition DOI: 10.1002/anie.201403769 Article first published online: 12 JUN 2014

© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

One final note, Friedrich Schiller University Jena is also known as the University of Jena.