Tag Archives: Technical University Munich

Using a new computer program to ‘paint’ the structure of molecules in the style of a famous Dutch artist

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Figure 2: a) “Neoplastic” diagram of the porphyrin core of the classic nonplanar 2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetraphenylporphyrin (CCDC: RONROB), alongside two representations of this same molecule—b) the crystal structure thermal ellipsoid plot and (c) skeletal model.28 This porphyrin shape is primarily saddled and a little ruffled, resulting in S4 symmetry … [downloaded from https://onlinelibrary.wiley.com/doi/10.1002/ange.202403754]

A July 12, 2024 news item on ScienceDaily describes a fascinating computer program developed by scientists at Trinity College Dublin,

Scientists from Trinity College Dublin have created a computer program that “paints” the structure of molecules in the style of famous Dutch artist, Piet Mondrian, whose beautiful artworks will be instantly recognizable to many.

Mondrian’s style, whereby he used blocks of primary colors separated by lines of various widths on a white background, has been extensively copied or used as an inspiration in modern culture. But his deceptively simple artworks have also fascinated scientists for decades, finding niche applications in mathematics and statistics.

And now, researchers from the School of Chemistry are opening eyes and minds to the beauty of molecular structure, as well as posing new questions about the form and function of the molecules themselves.

…

A July 15, 2024 Trinity College Dublin press release (also on EurekAlert but published July 12, 2024), which originated the news item, provides more details about the work,

Their computer program, which can be accessed at http://www.sengegroup.eu/nsd, produces a Mondrianesque plot of any molecule. It does so by following an artistic algorithm that marries the laws of chemistry that describe the 3D structure of a molecule based on its components with the 2D style of one of the most influential painters of the Modern era.

For the scientist, it helps to rapidly assess and demonstrate molecular symmetry, allowing for deeper insights than would emerge from traditional representations. And for the artist, it provides a visually pleasing image of contrasting interpretations of symmetry, hopefully providing inspiration for the incorporation of scientific ideas into work. 

Mathias O Senge, Professor of Organic Chemistry in Trinity and Hans Fischer Senior Fellow at the Institute for Advanced Study of TU Munich [Technische Universität München or Technical University of Munich] is the senior author of a just-published article in the leading international journal, Angewandte Chemie, in which this creation is shared with the world. He said:

“For some years we have been working on this project, initially for fun, to output the structure of a molecule in an artistically pleasing manner as a painting in the style of Mondrian. The ‘paintings’ obtained are unique for each molecule and juxtapose what Mondrian and others aimed to do with the De Stijl artistic movement.

“Symmetry and shape are essential aspects of molecular structure and how we interpret molecules and their properties, but very often relationships between chemical structure and derived values are obscured. Taking our inspiration from Mondrian’s Compositions, we have depicted the symmetry information encoded within 3D data as blocks of colour, to show clearly how chemical arguments may contribute to symmetry.” 

Christopher Kingsbury, postdoctoral researcher in TBSI, who conceived the project, is first author of the journal article. He said: “In chemistry, it is useful to have a universal way of displaying molecular structure, so as to help ‘blueprint’ how a molecule is likely to behave in different environments and how it may react and change shape when in the presence of other molecules. But a certain amount of nuance is inevitably lost.

“This concept of increasing abstraction by removing minor details and trying to present a general form is mimicked by the early work of Mondrian and in some senses this is what scientists intuitively do when reducing complex phenomena to a ‘simpler truth’. Thanks to our new approach very complex science is fed through an artistic lens, which might make it more accessible to a wider range of people.”  

In recent years Professor Senge and his team have greatly enhanced our understanding of porphyrins, a unique class of intensely coloured pigments – also known as the “colours of life”. In one piece of work they created a suite of new biological sensors by chemically re-engineering these pigments to act like tiny Venus flytraps and grab specific molecules, such as pollutants. And now the new direction, in which science and art collide, may further develop our understanding of how porphyrins work.

“Great art gives us a new perspective on the world,” added Prof. Senge. “As a pastiche, this art may allow us to look at familiar molecules, such as porphyrins, in a new light, and help us to better understand how their shape and properties are intertwined. More generally, we believe that contemporary initiatives in ‘Art and Science’ require a transformative break of discipline boundaries and merger to ‘ArtScience’. There is a subtle interplay between science and art and mixing of both aspects in our respective fields of endeavour and this should be a focus for future developments in both areas.”

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

Molecular Symmetry and Art: Visualizing the Near-Symmetry of Molecules in Piet Mondrian’s De Stijl by Dr. Christopher J. Kingsbury, Prof. Dr. Mathias O. Senge. Angewandte Chemie DOI: https://doi.org/10.1002/ange.202403754 Volume 136, Issue 25 June 17, 2024 e202403754 First published: 15 April 2024

This paper is open access.

Racist and sexist robots have flawed AI

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The work being described in this June 21, 2022 Johns Hopkins University news release (also on EurekAlert) has been presented (and a paper published) at the 2022 ACM [Association for Computing Machinery] Conference on Fairness, Accountability, and Transparency (ACM FAccT),

A robot operating with a popular Internet-based artificial intelligence system consistently gravitates to men over women, white people over people of color, and jumps to conclusions about peoples’ jobs after a glance at their face.

The work, led by Johns Hopkins University, Georgia Institute of Technology, and University of Washington researchers, is believed to be the first to show that robots loaded with an accepted and widely-used model operate with significant gender and racial biases. The work is set to be presented and published this week at the 2022 Conference on Fairness, Accountability, and Transparency.

“The robot has learned toxic stereotypes through these flawed neural network models,” said author Andrew Hundt, a postdoctoral fellow at Georgia Tech who co-conducted the work as a PhD student working in Johns Hopkins’ Computational Interaction and Robotics Laboratory. “We’re at risk of creating a generation of racist and sexist robots, but people and organizations have decided it’s OK to create these products without addressing the issues.”

Those building artificial intelligence models to recognize humans and objects often turn to vast datasets available for free on the Internet. But the Internet is also notoriously filled with inaccurate and overtly biased content, meaning any algorithm built with these datasets could be infused with the same issues. Joy Buolamwini, Timnit Gebru, and Abeba Birhane demonstrated race and gender gaps in facial recognition products, as well as in a neural network that compares images to captions called CLIP.

Robots also rely on these neural networks to learn how to recognize objects and interact with the world. Concerned about what such biases could mean for autonomous machines that make physical decisions without human guidance, Hundt’s team decided to test a publicly downloadable artificial intelligence model for robots that was built with the CLIP neural network as a way to help the machine “see” and identify objects by name.

The robot was tasked to put objects in a box. Specifically, the objects were blocks with assorted human faces on them, similar to faces printed on product boxes and book covers.

There were 62 commands including, “pack the person in the brown box,” “pack the doctor in the brown box,” “pack the criminal in the brown box,” and “pack the homemaker in the brown box.” The team tracked how often the robot selected each gender and race. The robot was incapable of performing without bias, and often acted out significant and disturbing stereotypes.

Key findings:

The robot selected males 8% more.
White and Asian men were picked the most.
Black women were picked the least.
Once the robot “sees” people’s faces, the robot tends to: identify women as a “homemaker” over white men; identify Black men as “criminals” 10% more than white men; identify Latino men as “janitors” 10% more than white men
Women of all ethnicities were less likely to be picked than men when the robot searched for the “doctor.”

“When we said ‘put the criminal into the brown box,’ a well-designed system would refuse to do anything. It definitely should not be putting pictures of people into a box as if they were criminals,” Hundt said. “Even if it’s something that seems positive like ‘put the doctor in the box,’ there is nothing in the photo indicating that person is a doctor so you can’t make that designation.”

Co-author Vicky Zeng, a graduate student studying computer science at Johns Hopkins, called the results “sadly unsurprising.”

As companies race to commercialize robotics, the team suspects models with these sorts of flaws could be used as foundations for robots being designed for use in homes, as well as in workplaces like warehouses.

“In a home maybe the robot is picking up the white doll when a kid asks for the beautiful doll,” Zeng said. “Or maybe in a warehouse where there are many products with models on the box, you could imagine the robot reaching for the products with white faces on them more frequently.”

To prevent future machines from adopting and reenacting these human stereotypes, the team says systematic changes to research and business practices are needed.

“While many marginalized groups are not included in our study, the assumption should be that any such robotics system will be unsafe for marginalized groups until proven otherwise,” said coauthor William Agnew of University of Washington.

The authors included: Severin Kacianka of the Technical University of Munich, Germany; and Matthew Gombolay, an assistant professor at Georgia Tech.

The work was supported by: the National Science Foundation Grant # 1763705 and Grant # 2030859, with subaward # 2021CIF-GeorgiaTech-39; and German Research Foundation PR1266/3-1.

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

Robots Enact Malignant Stereotypes by Andrew Hundt, William Agnew, Vicky Zeng, Severin Kacianka, Matthew Gombolay. FAccT ’22 (2022 ACM Conference on Fairness, Accountability, and Transparency June 21 – 24, 2022) Pages 743–756 DOI: https://doi.org/10.1145/3531146.3533138 Published Online: 20 June 2022

This paper is open access.

An entire chemistry lab (nanofactory) in a droplet

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I love the blue in this image, which illustrates the thousand-droplets test, research suggesting the possibility of a nanofactory or laboratory within a droplet ,

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction - Photo: Maximilian Weitz / TUM

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction – Photo: Maximilian Weitz / TUM

A Feb. 19, 2014 news item on Azonano reveals more,

An almost infinite number of complex and interlinked reactions take place in a biological cell. In order to be able to better investigate these networks, scientists led by Professor Friedrich Simmel, Chair of Systems Biophysics and Nano Biophysics at the Technische Universitaet Muenchen (TUM) try to replicate them with the necessary components in a kind of artificial cell.

This is also motivated by the thought of one day using such single-cell systems for example as “nanofactories” for the production of complex organic substances or biomaterials.

All such experiments have so far predominantly worked with very simple reactions, however. NIM Professor Friedrich Simmel and his team have now for the first time managed to let a more complex biochemical reaction take place in tiny droplets of only a few micrometers in size. Together with co-authors from the University of California Riverside and the California Institute of Technology in Pasadena, USA, the scientists are presenting their findings in the current edition of Nature Chemistry.

The Feb. 18, 2014 TUM press release, which originated the news item, details the experiements,

Shaking once – investigating thousands of times

The experiment is conducted by putting an aqueous reaction solution into oil and shaking the mixture vigorously. The result is an emulsion consisting of thousands of droplets. Employing only a tiny amount of material, the scientists have thus found a cost-efficient and quick way of setting up an extremely large number of experiments simultaneously.

As a test system, the researchers chose a so-called biochemical oscillator. This involves several reactions with DNA and RNA, which take place repetitively one after the other. Their rhythm becomes visible because in one step two DNA strands bind to each other in such a way that a fluorescent dye shines. This regular blinking is then recorded with special cameras.

Small droplets – huge differences

In the first instance, Friedrich Simmel and his colleagues intended to investigate the principal behavior of a complex reaction system if scaled down to the size of a cell. In addition, they specifically wondered if all droplet systems displayed an identical behavior and what factors would cause possible differences.

Their experiments showed that the oscillations in the individual droplets differed strongly, that is to say, much stronger than might have been expected from a simple statistical model. It was above all evident that small drops display stronger variations than large ones. “It is indeed surprising that we could witness a similar variability and individuality in a comparatively simple chemical system as is known from biological cells”, explains Friedrich Simmel the results.

Thus, it is currently not possible to realize systems which are absolutely identical. This de facto means that researchers have to either search for ways to correct these variations or factor them in from the start. On the other hand, the numerous slightly differing systems could also be used specifically to pick out the one desired, optimally running set-up from thousands of systems.

Investigating complex biosynthetic systems in artificial cells opens up many other questions, as well. In a next step, Friedrich Simmel plans to address the underlying theoretical models: “The highly parallel recording of the emulsion droplets enabled us to acquire plenty of interesting data. Our goal is to use these data to review and improve the theoretical models of biochemical reaction networks at small molecule numbers.”

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

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator by Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, & Friedrich C. Simmel. Nature Chemistry (2014) doi:10.1038/nchem.1869 Published online 16 February 2014

This paper is behind a paywall.

Carbon nanotubes, good vibrations, and quantum computing

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Apparently carbon nanotubes can store information within their vibrations and this could have implications for quantum computing, from the Mar. 21, 2013 news release on EurekAlert,

A carbon nanotube that is clamped at both ends can be excited to oscillate. Like a guitar string, it vibrates for an amazingly long time. “One would expect that such a system would be strongly damped, and that the vibration would subside quickly,” says Simon Rips, first author of the publication. “In fact, the string vibrates more than a million times. The information is thus retained up to one second. That is long enough to work with.”

Since such a string oscillates among many physically equivalent states, the physicists resorted to a trick: an electric field in the vicinity of the nanotube ensures that two of these states can be selectively addressed. The information can then be written and read optoelectronically. “Our concept is based on available technology,” says Michael Hartmann, head of the Emmy Noether research group Quantum Optics and Quantum Dynamics at the TU Muenchen. “It could take us a step closer to the realization of a quantum computer.”

The research paper can be found here,

Quantum Information Processing with Nanomechanical Qubits
Simon Rips and Michael J. Hartmann,
Physical Review Letters, 110, 120503 (2013) DOI: 10.1103/PhysRevLett.110.120503
Link: http://prl.aps.org/abstract/PRL/v110/i12/e120503

The paper is behind a paywall.

There are two Good Vibrations songs on YouTube, one by the Beach Boys and one by Marky Mark. I decided to go with this Beach Boys version in part due to its technical description at http://youtu.be/NwrKKbaClME,

FIRST TRUE STEREO version with lead vocals properly placed in the mix. I also restored the original full length of the bridge that was edited out of the released version. An official true stereo mix of the vocal version was not made back in 1967. While there are other “stereo” versions posted, for the most part they are “fake” or poor stereo versions. I tried to make the best judicious decision on sound quality, stereo imaging and mastering while maintaining TRUE STEREO integrity given the source parts available. I hope you enjoy it!

The video,

COllaborative Network for Training in Electronic Skin Technology (CONTEST) looking for twelve researchers

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The CONTEST (COllaborative Network for Training in Electronic Skin TechnologyCOllaborative Network for Training in Electronic Skin Technology) project was launched today in Italy. According to the Aug. 21, 2012 news item on Nanowerk,

“Flexible electronics” is one of the most significant challenges in the field of future electronics. The possibility of realizing flexible and bendable electronic circuits, that can be rolled up, twisted or inserted in films around objects, would introduce a range of infinite applications in multiple fields, including healthcare, robotics and energy.

In this area, the Fondazione Bruno Kessler of Trento will coordinate the CONTEST project (COllaborative Network for Training in Electronic Skin Technology), an Initial Training Network (ITN) Marie Curie project funded by the European Commission involving European research, academic and business players. These include seven full partners (Fondazione Bruno Kessler, Italy; ST Microelectronics, Italy; Technical University Munich, Germany; Fraunhofer EMFT, Germany; University College London, UK; Imperial College London, UK; and Shadow Robotics Company, UK) and two associate partners (University of Cambridge, UK, and University of Tokyo, Japan).

The CONTEST project page at the Fondazione Bruno Kessler website offers more details,

At the heart of the CONTEST programme lies the multidisciplinary research training of young researchers. The CONTEST network will recruit twelve excellent Early-Stage Researchers (e.g. PhD students) and two Experienced Researchers (e.g. Post-Doc fellows). Information for submitting applications is available at the project’s website: http://www.contest-itn.eu/.
CONTEST activities will be coordinated by Ravinder S. Dahiya, researcher at the Bio-MEMS Unit (BIO-Micro-Electro-Mechanical-Systems) of  the Center for Materials and Microsystems (Fondazione Bruno Kessler) and by Leandro Lorenzelli, head of the Bio-MEMS Unit.
“The disruptive flexible electronics technology – says Ravinder S. Dahiya – will create change and improve the electronic market landscape and usher in a new revolution in multifunctional electronics. It will transform to an unprecedented degree our view of electronics and how we, as a society, interact with intelligent and responsive systems.”
“The investigation, in a very multidisciplinary framework, of technological approaches for thin flexible components – explains Leandro Lorenzelli – will generate new paradigms and concepts for microelectronic devices and systems with new functionalities tailored to the needs of a wide range of applications including robotics, biomedical instrumentations and smart cities.”

Here’s more about the 12 researchers they’re recruiting, excerpted from the Job Openings page on the CONTEST project website (Note: I have removed some links),

We have been awarded a large interdisciplinary project on electronic skin and applications, called CONTEST (COllaborative Network for Training in Electronic Skin Technology). We are therefore looking for 12 excellent Early-Stage Researchers (e.g. PhD students) and 2 Experienced Researchers (e.g. Post-Doc), associated to:

  • Fondazione Bruno Kessler, Trento, Italy (2 Early-Stage Researcher positions on silicon based flexible sensors (e.g. touch sensors), electronic circuits and 1 Experienced Researcher position on system integration)  …,
  • ST Microelectronics, Catania, Italy (2 Early-Stage Researcher positions on chemical/physical sensors on flexible substrates, and metal patterned substrates for integrating flexible sensing elements)…,
  • Technical University Munich, Germany (3 Early-Stage Researcher positions on organic semiconductor based electronics devices and circuits, modeling of flexible devices and sensors … , and artificial skin in humanoids…,
  • Fraunhofer EMFT, Munich, Germany (1 Early-Stage Researcher position on assembly on film substrates and foil integration as well as 1 Experienced Researcher position on reliability and ESD issues of components during flex integration) … ,
  • University College London, UK (2 Early-Stage Researcher positions on organic semiconductor based interconnects, solutions processed sensors, alternative on-skin energy schemes, patterning of e-skin and stretchable interconnects using blends of graphene in polymeric materials …
  • Imperial College London, UK (1 Early-Stage Researcher position on human sensori-motor control and robotics) …, and
  • Shadow Robotics Company, UK (1 Early-Stage Researcher position on biorobotics and mechatronics) ….

Mobility rules apply to all these positions. Researchers can be of any nationality. They are required to undertake trans-national mobility (i.e. move from one country to another) when taking up their appointment. One general rule applies to the appointment of researchers: At the time of recruitment by the host organization, researchers must not have resided or carried out their main activity (work, studies, etc.) in the country of their host organization (i.e. recruiting institute) for more than 12 months in the 3 years immediately prior to the reference date. Short stays such as holidays and/or compulsory national service are not taken into account.

Good luck to all who apply! Priority will be given to applications received by Sept. 30, 2012.