There is an urgent need to develop safer, more effective, and personalized treatments for these kidney disorders. With mathematicians from Oxford, Heather Harrington, Professor of Mathematics at the TU Dresden and the University of Oxford and Director at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, and the Center for Systems Biology Dresden (CSBD), developed new mathematical approaches to quantify data from new experimental technologies. 

Tools that allow scientists to understand gene expression in individual cells after separating them from a kidney sample have been around for about ten years, but very recently, new techniques are starting to reveal these cell signatures in a tissue context. This means the cells can be considered part of their local neighborhood, showing how cells move and signal to each other. This approach is exciting for autoimmune kidney diseases like lupus because the kidney is complex with more than 30 types of cells, and in lupus these are joined by multiple immune cell types, yet how these interactions lead to kidney damage is not well understood.

Aneesha Bhandari, supervised by Oxford Principal Investigator and Nephrologist Dr. Katherine Bull, has been using these new spatial methods to look at lupus kidney disease, but Katherine and Aneesha encountered a problem: the spatial information is at unprecedented subcellular resolution but very sparse and noisy, so deciding what type of cells they had found and where the boundary of each cell lies was challenging with these new methods. They knew there must be a way to dynamically use the local expression information to improve this, but how? Luckily, a conversation with mathematicians Professors Heather Harrington and Ulrike Tillmann and their student Katherine Benjamin revealed an elegant solution. Their research in topological data analysis identifies spatial patterns in data across different parameters. Together, the teams developed a new method, TopACT, to apply this mathematics to the spatial kidney data. They were able to reveal hidden patterns in the lupus kidney, with immune cells circling the glomerular regions. The approach turns out to work on a range of spatial platforms, which is important as these technologies are moving fast and could be applied in the future to 3-dimensional data.

Katherine Bull says, “This is a really interdisciplinary effort between mathematics and biology, allowing us to see granular detail and hidden patterns of inflammation in the kidney in lupus. These tools are an important step towards developing more targeted ways to treat this complex disease.”

Heather Harington says, “We are excited that this new spatial transcriptomics technology required us to develop novel mathematical approaches, building upon state-of-the-art topological data analysis. In this work, we identified spatial locations of sparse cells and then generated a hypothesis of a ring of immune cells in mouse kidney tissue, which was experimentally verified. Trying to understand this complex biological data offers interesting and challenging mathematical opportunities.”

The team challenge participation is a component of MPI-CBG's Health Initiative, which aims to enhance employee wellbeing. Measures covering a wide range of topics include physical education classes, mental health seminars, health screenings, and health days. The Max Planck Society's collaboration with Technische Krankenkasse makes many of these activities possible.

Congratulations to all participants in the team challenge!

Children can pipette or estimate the number of flies in a tube during Science Night at the MPI-CBG. There will be guided tours for children to see the zebrafish. At eleven science stations, visitors can have a look at miniature liver models, learn about embryonic stem cells, transgenic mice, and animal welfare, see the smallest structures in a cell, and find water creatures in the institute's pond and identify them with researchers. You can observe forces within developing embryos, learn how researchers understand how our organs grow to acquire the size and shape that fits the body, learn about sustainable science, discover the architecture of the liver, or see stem cells from various animals under the microscope, from which researchers learn about the pregnancy length in different animals. At two stations, you learn all about proteins, the power tools in the smallest factory in the world: the cell. Isolate proteins yourself and predict the structure and function of proteins using computers. Prof. Wieland Huttner will give a talk at 6 p.m. on the development of the human brain and what distinguishes us from Neanderthals.

This year, we offer guided tours in Russian, Ukrainian, and Arabic at our science stations. Interested people can ask at the reception desk for a guide.

Once a year, Dresden's universities, non-university research institutions, and science-related businesses open their doors to the general public. Interested visitors will be able to experience science and technology, research and innovation, art, and culture through a variety of lectures, experiments, guided tours, displays, and films. We are looking forward to your visit!

The full program at the MPI-CBG is available here.
The program of the Dresden Long Night of Science can be found here.

The event started at 2 p.m. with star processions at four locations: Fritz-Foerster-Platz, Sachsenplatz, Albertplatz, and Wettiner Platz. The MPI-CBG took off with the star procession from Sachsenplatz, where a Johannstadt Statement [link] by the scientific and cultural institutions was presented. The participants of the four-star processions arrived at the Altmarkt at around 3 p.m., where they met many visitors, who already gathered between the main stage and the pavilions with an accompanying scientific and artistic program.

The program on stage and the supporting program in ten pavilions provided visitors with information on topics ranging from internationality in science, where the MPI-CBG was involved, to action art and the didactics of democracy. Each of the pavilions featured opportunities to exchange ideas with researchers and artists and to celebrate democracy together.

“For the first time, science and culture, together with citizens, are sending a signal for the protection of our liberal democratic system," said Prof. Ursula Staudinger, Rector of the TUD, who emphasized the crucial importance of democracy for living together in peace and freedom in her opening speech at the start of the main event on the Altmarkt. "We are living in a time in which our democracy is being deliberately undermined and threatened. We must fight the beginnings. Our liberal democracy cannot be taken for granted. It must be lived and protected each and every day. That's why we want to engage in respectful discussions on stage today and at the pavillions on exciting topics relating to our democracy, even when opinions differ,” continued Rector Prof. Staudinger.

The stage program included the musical statement "#LautSein" by the Dresdner Sinfoniker, which was specially developed for the occasion, as well as musical contributions by the Hamburg musician BOSSE. The event was moderated by MDR presenter Sissy Metzschke and science communicator Simon Hauser.

A clear position: open and solidary cooperation
In addition to the Rector of the TUD, the democracy festival of science, art, and culture was opened by Prof. Gerhard Rödel, Managing Director of DRESDEN-concept e. V. and speaker of the international graduate school DIGS-BB, Joachim Klement, Director of the Staatsschauspiel, and Christiane Mennicke-Schwarz, Director of the Kunsthaus Dresden.

"Dresden is a great research location, in part thanks to the many outstanding researchers who come to us from all over the world. With today's event, we want to show how important it is to us and the thousands of participants that they can live and work freely and without discrimination in our country and in our city in the spirit of our constitution," said Prof. Gerhard Rödel.

"Diversity is our strength"
Joachim Klement emphasized the importance of the German constitution and demonstrating a firm stance: "Our times demand a clear stance! Today, it is more important than ever to stand up for open and solidary coexistence. 75 years after the creation of the constitution and 35 years after the peaceful autumn of 1989, science and culture form a counterweight to hatred and populism," says Klement. "We are showing that diversity is our strength. Together, we are sending a clear signal for democracy and our fundamental rights. Together, we stand for an open country - and for a new way of living together," continued Klement.

Overwhelming commitment
Christiane Mennicke-Schwarz took the opportunity to thank the participants and supporters for their outstanding commitment to democracy: "We are overwhelmed by the huge voluntary engagement of everyone involved. In addition to the common goal of standing up for democracy, this also shows a growing network between science and culture in Dresden," said Christiane Mennicke-Schwarz, Director of the Kunsthaus Dresden.

International science
Stephan Grill, Director at the Max Planck Institute of Molecular Cell Biology and Genetics, said on stage: “Dresden is an excellent science location, and science thrives on internationality and an open society, and this must be maintained. We need international scientists in Dresden and that requires an open-minded society.”

News article originally published by the TU Dresden: https://tu-dresden.de/tu-dresden/newsportal/news/gemeinsam-fuer-demokratie-rund-2-500-menschen-setzten-starkes-zeichen-fuer-vielfalt-freiheit-und-ein-respektvolles-miteinander?set_language=de

The event started at 2 p.m. with star processions at four locations: Fritz-Foerster-Platz, Sachsenplatz, Albertplatz, and Wettiner Platz. The MPI-CBG took off with the star procession from Sachsenplatz, where a Johannstadt Statement by the scientific and cultural institutions that are located in the area was presented.

The research group of Agnes Toth-Petroczy at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD) together with the mass spectrometry experts from the research group of Andrej Shevchenko at the MPI-CBG wanted to understand how often cells make mistakes when reading stop signs in their genetic instructions and how temperature and nutrient depletion affects these mistakes. In their new study published in Nature Communications, the researchers examined how common these errors are, what factors might influence them, and where they come from.

Maria Luisa Romero Romero, the lead author of the study, explains, “We looked at the frequency of stop codon reading errors and if and how environmental circumstances affect them. To find this out, we put stop codons into the middle of a fluorescent protein and placed it inside E. coli bacteria. Then, we used microscopy, mass spectrometry and RNA-sequencing to observe these mistakes. We found that when cells are stressed, these errors can happen a lot, up to 80% of the time, depending on the specific genetic instructions.”

Furthermore, the data shows that temperature and nutrient depletion can influence how often stop codon recoding happen in cells. This means that environmental factors can affect how accurately cells make proteins, leading to diverse set of proteins when cells need to adapt to different conditions.

“Overall, our study shows that cells often make mistakes when producing proteins, especially when they are stressed,” explains Agnes Toth-Petroczy, who supervised the study. “We think that bacteria may be able to quickly diversify the sequences of their proteins in order to respond to abrupt changes in their environment by using stop codon recoding as a mechanism.”

Sandra says: “Our goal is to understand how tissue renewal is driven by the organization of endomembrane organelles and how age can affect this. The organ that we use to address this is super fascinating: it's the small intestine. In the small intestine, adult stem cells constantly transport signals along their endomembrane organelles to communicate with their microenvironment, and based on this crosstalk, they make the decision to divide and constantly replace old cells with new cells. The difficulty is that as we age, our ability to renew tissue decreases since our stem cells lose some of their functionality. They are unable to properly renew our intestines, which can cause diseases such as intestinal inflammation or cancer. Our goal is to eventually gain the information necessary to identify and correct the dysfunctions that come with aging.”

Welcome to the institute, Sandra!

Sandra has an educational background in Cell and Molecular Biology. During her PhD at the EMBL Heidelberg in Germany, she studied the secretory membrane machinery regulation of cells using imaging-based membrane transport assays. In 2016, Sandra moved to the Karolinska Institute in Stockholm, Sweden, for her postdoctoral studies, where she translated her membrane biology knowledge to the tissue level. She focused her research on the organization of secretory membrane organelles in adult tissue stem cells and developed approaches in 3D organoid culture systems to study membrane transport in stem cell-mediated tissue renewal.

Together, we want to send a clear signal for democracy and our constitutional rights: the dignity of every human being is inviolable, and the voices of minorities are heard. For us, these are things that are taken for granted but they are increasingly under threat. Together, we want to protect these fundamental values of our democratic and open society. The freedom of science and art is fundamental for a society that wishes to overcome the major challenges of our time.

We invite you to join us!

Join us in our commitment to democracy! Starting at 2 p.m., several groups will move to the Altmarkt in four-star trains. The Max Planck Institute of Molecular Cell Biology and Genetics will start with the star procession from Sachsenplatz. A stage program with speeches and music will take place at the Altmarkt. There, we would like to encourage encounters and discussions through various scientific and artistic exchange formats. Tell us about your experiences, let us discuss together why democratic principles are essential for science to be successful. Everyone is welcome to join us in working for democracy.

More information: https://dresden-concept.de/demokratie/?lang=en

The Leopoldina recognized Marino Zerial for his outstanding achievements in the field of cell biology and elected him to the section Genetics, Molecular Biology, and Cell Biology. One of his most significant discoveries is about the key role of the Rab5 protein in the molecular mechanisms of endocytosis and membrane transport.

Prior to his membership in the Leopoldina, Marino Zerial was awarded the Gottfried Wilhelm Leibniz Prize in 2008 and has been honored with the membership of the Istituto Veneto di Scienze, Lettere ed Arti in 2019. In 2021, he became an International Honorary Member of the American Academy of Arts and Sciences.

“The election to Leopoldina is a great honor for me,” says Marino Zerial. “I am excited for the chance to join the oldest Academy in life science and for the chance to contribute my knowledge to policymakers and society.” Zerial joins current MPI-CBG Director Prof. Anthony Hyman and former MPI-CBG directors Prof. Wieland Huttner, Prof. Elisabeth Knust, Prof. Kai Simons, and Prof. Eugene Myers as members of the Academy.

As the German National Academy of Sciences, the Leopoldina provides independent science-based policy advice on socially relevant issues. For this purpose, the Academy develops interdisciplinary statements based on scientific findings. The Leopoldina represents German science in international bodies, including science-based advice to the annual G7 summits. It has 1,600 members from more than 30 countries and brings together expertise from almost all fields of research. It was founded in 1652 and was named Germany's National Academy of Sciences in 2008. Each year, about 50 scientists are elected to the Academy for life in a multi-step selection process. Since the academy was founded, more than 7,000 individuals have been accepted into its ranks. Among them were Marie Curie, Charles Darwin, Albert Einstein, Johann Wolfgang von Goethe, Alexander von Humboldt, Justus von Liebig, and Max Planck.

A remarkable scientific program was organized, involving a panel of twenty speakers and numerous local and foreign guests from all stages of his career, including amongst others Alpha Yap (University of Queensland), Suzanne Pfeffer (Stanford University), Tomas Kirchhausen (Harvard Medical School), Satyajit Mayor (National Centre for Biological Sciences, Bangalore), and Ira Mellman (Geneentech). The program was touching and exciting since so many people contributed happy memories and personal anecdotes.

Marino Zerial studied at the University of Trieste and was awarded a Doctor Degree in Biology there in 1982. He did his postdoctoral work at the Institut J. Monod, Paris, and at the European Molecular Biology Laboratory (EMBL), Heidelberg, where he was appointed research group leader at the Cell Biology Program in 1991. He was awarded the Gottfried Wilhelm Leibniz Prize in 2008 and has been honored with the membership of the Istituto Veneto di Scienze, Lettere ed Arti in 2019. In 2021, he became an International Honorary Member of the American Academy of Arts and Sciences.

Originally trained as a physicist, Pierre transitioned to the field of quantitative biology during his PhD at the École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI). His postdoctoral research at the University of Amsterdam and IBDM Marseille focused on deciphering the complexities of cellular organization using super-resolution microscopy. Pierre remarks about his research, “The organization of the cell is often hypothesized rather than directly observed. With the rise of super-resolution methods, reaching a novel understanding of cell organization is now possible. Techniques such as DNA-PAINT can achieve a resolution of 5 nanometers, enabling us to uncover the organization of the developing muscle.”

Regarding the ELBE visiting faculty program, he expresses, “The research focus of MPI-CBG and CSBD aligns with my interests: exploring developmental biology through the integration of experimental and theoretical approaches. In this hiatus from teaching, I aim to focus on research and delve into new topics such as utilizing deep learning for data analysis.” During his stay in Dresden, Pierre is looking forward to the exchange of innovative ideas and opportunities to form new collaborations. He holds a particular interest in employing deep learning methodologies for denoising and automating image analysis. Additionally, he aims to develop spatial transcriptomics as a means to further explore morphogenesis in biological systems. He says, “People interested in super-resolution imaging techniques as well as image analysis and modeling should reach out to me.”

The ELBE Visiting Faculty Program at the CSBD continuously offers funded opportunities for researchers working in the area of its mission. During their stay, visiting faculty closely interact with research groups at the CSBD, with labs at the MPI-CBG, and with the Max Planck Institute for the Physics of Complex Systems (MPIPKS).

Congratulations!

As the fundamental cellular mechanisms and tissue behaviors are shared across living organisms, the jellyfish provides a simplified platform for understanding complex regenerative processes and the emerging properties of real, living tissues. “I am very happy to be part of the HFSP community through this funding. Here in Dresden, my group and I plan to build the theoretical framework for both regenerative medicine and the properties of self-healing materials,” explains Carl Modes. “These models will be based on geometric and topological aspects of theoretical biophysics and computational biology, and we hope they will enable us to capture how different classes of injuries affect regeneration.”

For 2024, HFSP has chosen to support 34 Research Grant  project teams (Program Grants and Early Career Grants) that include 108 scientists representing 23 nations. Each grant will last for three years and on average, each award is for $400,000 USD per year. For their awards, the HFSP seeks scientists who form internationally, preferably intercontinentally, collaborative teams, who have not worked together before, and who are engaging in work for which they have no preliminary data. In this regard, HFSP fosters frontier research and science diplomacy.

Congratulations to all 2024 winners!

Press Release HFSP

Jinghui explains: “In my project, I want to uncover the dynamic electrical environmental changes that cells are exposed to upon organ damage and how these can be coupled with biochemical signaling towards the start of proliferation. By working with the regenerating zebrafish larval fin as a model, my goal is to establish quantitative approaches across length and time scales that can have a broad impact in the emerging field of bioelectricity. This is a highly interdisciplinary project that relies on strong interactions with, amongst others, the research group of Frank Jülicher at the Max Planck Institute for the Physics of Complex Systems.”

MSCA Postdoctoral Fellowships enhance the creative and innovative potential of researchers holding a PhD and wishing to acquire new skills through advanced training and international, interdisciplinary, and inter-sectoral mobility. The funding supports researchers ready to pursue frontier research and innovation projects in Europe and worldwide, including in the non-academic sector.

Congratulations, Jinghui!

Press Release of the European Commission: https://marie-sklodowska-curie-actions.ec.europa.eu/news/marie-sklodowska-curie-actions-award-eu260-million-to-postdoctoral-researchers-in-2023

Three researchers, Cedric Landerer, Jonas Poehls and, Agnes Toth-Petroczy from the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and the Center for Systems Biology Dresden (CSBD), now present the first study that shows how protein-making mistakes are distributed in the proteome (the entire set of proteins), how often they happen, and what the wrong protein means for the health and functionality of a cell.

The first author of the study, Cedric Landerer, explains, “We studied two organisms, the bacterium E. coli and S. cerevisiae (also known as brewer’s or baker’s yeast), and found that about 20–23% of all proteins in these cells could have at least one mistake in them. Interestingly, harmful mistakes were less common. We trained our model using data from mass spectrometry experiments that detected these mistakes.”

“In general, it seems that the cells we studied have a pretty good system in place to handle mistakes during protein-making,” says research group leader Agnes Toth-Petroczy. “With our  pipeline and the mechanistic model, we can now explore how accurate protein-making is for many different species. We can also look at how protein-making accuracy changes in different situations, like when cells are stressed or during diseases.”

Kai Simons says, “The book is about my scientific journey, especially about my experience of building research environments, how I first helped to build up the new Haartman Institute in Helsinki, then the “Cell Biology Program” at the European Molecular Biology Laboratories (EMBL) in Heidelberg, and finally, of course, the foundation of the MPI-CBG here in Dresden. I wanted to describe how we managed to establish multidisciplinary environments where it was easier to solve research problems through cooperation and to do that without too much unnecessary pressure - Happy MPI-CBG”. 

It was the COVID-19 pandemic that gave Kai Simons the push to write about his life as a scientist. Over the past years, he had filled many notebooks with the events of his life. During the lockdown, Kai read the notebooks again and was able to focus on his book. It took him three months to write the Swedish version of the book.

“I have written the book for young researchers to give them inspiration not only for doing research in general but also to give them ideas on how to improve their own research environments. Maybe one day someone will make use of the book as a guide for founding a new research institute. That would make me more than happy,” says Kai Simons.

Kai Simons was born in 1938 in Helsinki, Finland. In 1964, he graduated from the University of Helsinki as a medical doctor, followed by postdoctoral work at Rockefeller University in New York, USA. Back at the University of Helsinki, he was a professor in the area of biochemistry between 1971 and 1979, next to a position as investigator at the Finnish Medical Research Council from 1967 to 1975. Kai Simons joined the European Molecular Biology Laboratory in Heidelberg, Germany, in 1975 as a research group leader, where he then built up the Cell Biology Programme from 1982–1998. He was the managing director in the team of founding directors of the MPI-CBG. In 2006, he became Director Emeritus. Now he  is the CEO of Lipotype GmbH.

“The Magic of the Collective” book is available as e-book or as paperback.

The project Allergator aims to enable sustainable cat-keeping for families with cat-allergic members. In the next six months, the team of postdoctoral researchers Hendrik Sikkema and Benedikt Kuhn, along with technology development research group leader Eric Geertsma, will validate a relevant market need, define the technology and product roadmap, and build a strong team. Benedikt Kuhn explains: “For the most prominent cat allergen, Fel d 1, we have developed tiny binding proteins that neutralize the allergen and prevent it from triggering an immune response.”

With "Vulcan," postdoctoral researcher Juan Iglesias-Artola and former postdoctoral researcher Anatol Fritsch aim at commercializing temperature-controlled microscope stages accompanied by software that allows users to perform complex temperature experiments. Juan Iglesias-Artola explains, “Anatol and I have identified that light microscopy studies often require an accurate control of temperature. Most devices available, unfortunately, only allow for heating, change temperature slowly, and are not interchangeable between microscopes. They also do not offer a user interface that allows for exporting the temperature data over the course of the experiment. With our start-up, we aim at solving these issues.” Anyone who is interested in being part of the demo community can get in contact with the research team via email.

The Bulgarian Prime Minister, Nikolay Denkov, met with representatives of MPI-CBG and IMB in Sofia on December 5, 2023. Along with the project leader Stoyno Stoynov, the director of IMB, Anastas Gospodinov, MPI-CBG director Stephan Grill, and MPI-CBG technology development group leader, Mihail Sarov, they met with the Bulgarian prime minister. The participants at the meeting talked about the goals of BioMedRTC, which will investigate the molecular mechanisms behind rare genetic diseases, genetic stability maintenance, and the development of anti-cancer medications. It was mentioned at the meeting that the new center will be crucial to advancing research in Bulgaria in the fields of cancer and clinical genetics.

After their meeting with the Prime Minister, the researchers from MPI-CBG and the IMB met with the deputy minister of science and education of Bulgaria, Genka Petrova, and afterwards with the German ambassador in Bulgaria, Irene Maria Plank.

Following the successful first round of evaluation, funding of approximately 1.5 million euros has been granted by the National Roadmap for Scientific Infrastructure to prepare for the realization of the project’s vision. If the proposal succeeds in the next round of the competition, BioMedRТC is planned to be implemented from 2025 in Sofia, Bulgaria, with a funding of up to 15 million euros from the European Union and matching funding from the Bulgarian national government. The idea is to shape it after the models of the advanced partner institutes, MPI-CBG and the Curie Institute.

Machine learning is rapidly expanding and plays a crucial role in solving various problems, including in biophysics. Data analysis in life sciences stands to gain immensely from advanced tools developed by machine learning experts. The aim of the symposium was to bridge these two worlds and demonstrate how advanced techniques can significantly enhance research in different biological contexts.

The symposium included presentations on techniques and highlighted various examples of how to use machine learning as a tool to optimize and improve data analysis in different biology contexts. Local experts from the TU Dresden, the MPI-CBG, the Max Planck Institute for Mathematics in the Sciences (MPI MiS), the Helmholtz-Zentrum Dresden-Rossendorf (HZDR), and the National Center for Tumor Diseases Dresden (NCT/UCC) presented their ideas and research. The organizers of this symposium are hoping to create connections between people who are developing machine-learning tools and those with an interest in applying them to problems in biology and biological physics.

Biological processes and behaviors are often very complex. Physical theories provide a precise and quantitative framework for understanding them. The active matter theory offers a framework to understand and describe the behavior of active matter – materials composed of individual components capable of converting a chemical fuel (“food”) into mechanical forces. Several scientists from Dresden were key in developing this theory, among others Frank Jülicher, director at the Max Planck Institute for the Physics of Complex Systems, and Stephan Grill, director at the MPI-CBG. With these principles of physics, the dynamics of active living matter can be described and predicted by mathematical equations. However, these equations are extremely complex and hard to solve. Therefore, scientists require the power of supercomputers to comprehend and analyze living materials. There are different ways to predict the behavior of active matter, with some focusing on the tiny individual particles, others studying active matter at the molecular level, and yet others studying active fluids on a large scale. These studies help scientists see how active matter behaves at different scales in space and over time.

Solving complex mathematical equations
Scientists from the research group of Ivo Sbalzarini, TU Dresden Professor at the Center for Systems Biology Dresden (CSBD), research group leader at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), and Dean of the Faculty of Computer Science at TU Dresden, have now developed a computer algorithm to solve the equations of active matter. Their work was published in the journal “Physics of Fluids” and was featured on the cover. They present an algorithm that can solve the complex equations of active matter in three dimensions and in complex-shaped spaces. “Our approach can handle different shapes in three dimensions over time,” says one of the first authors of the study, Abhinav Singh, a studied mathematician. He continues, “Even when the data points are not regularly distributed, our algorithm employs a novel numerical approach that works seamlessly for complex biologically realistic scenarios to accurately solve the theory's equations. Using our approach, we can finally understand the long-term behavior of active materials in both moving and non-moving scenarios for predicting their dynamics. Further, the theory and simulations could be used to program biological materials or create engines at the nano-scale to extract useful work.” The other first author, Philipp Suhrcke, a graduate of TU Dresden’s Computational Modeling and Simulation M.Sc. program, adds, “thanks to our work, scientists can now, for example, predict the shape of a tissue or when a biological material is going to become unstable or dysregulated, with far-reaching implications in understanding the mechanisms of growth and disease.”

A powerful code for everyone to use
The scientists implemented their software using the open-source library OpenFPM, meaning that it is freely available for others to use. OpenFPM is developed by the Sbalzarini group for democratizing large-scale scientific computing. The authors first developed a custom computer language that allows computational scientists to write supercomputer codes by specifying the equations in mathematical notation and let the computer do the work to create a correct program code. As a result, they do not have to start from scratch every time they write a code, effectively reducing code development times in scientific research from months or years to days or weeks, providing enormous productivity gains. Due to the tremendous computational demands of studying three-dimensional active materials, the new code is scalable on shared and distributed-memory multi-processor parallel supercomputers, thanks to the use of OpenFPM. Although the application is designed to run on powerful supercomputers, it can also run on regular office computers for studying two-dimensional materials.

The Principal Investigator of the study, Ivo Sbalzarini, summarizes: “Ten years of our research went into creating this simulation framework and enhancing the productivity of computational science. This now all comes together in a tool for understanding the three-dimensional behavior of living materials. Open-source, scalable, and capable of handling complex scenarios, our code opens new avenues for modeling active materials. This may finally lead us to understand how cells and tissues attain their shape, addressing the fundamental question of morphogenesis that has puzzled scientist for centuries. But it may also help us design artificial biological machines with minimal numbers of components.”

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The computer code that support the findings of this study are openly available in the 3Dactive-hydrodynamics github repository located at https://github.com/mosaic-group/3Dactive-hydrodynamics

The open source framework OpenFPM is available at https://github.com/mosaic-group/openfpm_pdata

Related Publications for the embedded computer language and the OpenFPM software library:
https://doi.org/10.1016/j.cpc.2019.03.007
https://doi.org/10.1140/epje/s10189-021-00121-x