12th bwHPC Symposium

Session

Talks

Sep 24, 2026, 10:10 AM

M629 (Universität Konstanz)

28. From light-field data to whole-brain functional ensembles: a GPU- and HPC-accelerated pipeline for larval zebrafish on bwForCluster NEMO2

Dr Sophie Aimon (Universität Konstanz)

9/24/26, 10:10 AM

Talk (15 min)

Understanding how the vertebrate brain coordinates behavior requires recording its activity across the whole brain and at the speed of neural dynamics. We use light-field microscopy (LFM) to image behaving larval zebrafish volumetrically and at high frame rates, capturing calcium activity across the entire brain while the animal responds to visual stimuli and generates swimming, eye, and fin...

15. CMF Fracture Segmentator: ein nnU-Net zur automatisierten Segmentierung von Frakturen des Unterkiefers

Johannes Schulze (Bundeswehrkrankenhaus Ulm, Deutschland, Klinik für Mund-, Kiefer- und plastische Gesichtschirurgie; Universitätsklinikum Ulm, Deutschland, Klinik für Mund-, Kiefer- und Gesichtschirurgie)

9/24/26, 10:25 AM

Talk (15 min)

Einleitung
Die virtuelle OP-Planung (VSP) spielt eine zunehmende Bedeutung in der maxillofazialen Traumatologie. Voraussetzung dafür ist die Segmentierung von 3D-Bilddatensätzen zur Erstellung von 3D-Oberflächendaten. Es existiert bisher kein frei zugängliches System zur automatisierten Segmentierung und Fragmentseparierung von Unterkieferfrakturen anhand von CT-Datensätzen. Ziel ist es,...

19. Global metagenomic reconstruction of the chicken gut virome reveals 19,778 viral populations and spatial partitioning

Timur Yergaliyev (Hohenheim Center for Livestock Microbiome Research (HoLMiR, 620))

9/24/26, 10:40 AM

Talk (15 min)

The gastrointestinal tract of chickens harbors complex microbial communities that play vital roles in host nutrition, physiological development, and immune regulation [1]. While bacterial microbiomes in poultry have been extensively characterized, the viral communities, or virome, remain poorly understood. However, the virome has significant potential to alter bacterial communities through...

26. Signoff Circuit Simulations for Modern Chip-Design using Leading-Edge Design Tools on the bwHPC NEMO2 Cluster

Johannes Stark

9/24/26, 12:10 PM

Talk (15 min)

Due to high prototyping costs, modern semiconductor design relies on extensive signoff simulations to verify the electrical
performance and reliability of complex integrated circuits before production.
As technology nodes continue to shrink and circuit complexity grows, the computational requirements of these simulations can
become a significant bottleneck in the design...

32. Scaling Extended Genetic and Evolutionary Algorithms on HPC-Systems: Master-Slave versus Island Algorithms

Andreas Geyer-Schulz (Information Services and Electronic Markete (CIN-IEM), KIT)

9/24/26, 1:40 PM

Talk (15 min)

In this contribution we contrast parallelization of extended
genetic and evolutionary algorithms by global generational
parallelization (a master-slave architecture) with island
models (a message-passing architecture). The first class
of algorithms uses a single large population where mating of individuals
is unrestricted, whereas the second class of algorithms uses multiple
populations...

30. Atomistic modelling of structures and processes in electrochemical energy storage and conversion

Prof. Axel Groß (Universität Ulm)

9/24/26, 1:55 PM

Talk (15 min)

Processes in electrochemical energy storage and conversion are critical to mitigate the detrimental effects of global warming. We will show that atomistic simulations based on quantum chemical methods together with machine-learning approaches can contribute to improve, e.g., the ion mobility and stability of battery materials and the catalytic activity of electrochemical interfaces. Thus these...

22. Decoding the “sweet” talk: modeling the glycan code in bacterial infections

Olga Makshakova (Synthetic Biology of Signalling Processes Lab, Signalling Research Centers BIOSS and CIBSS, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany)

9/24/26, 2:10 PM

Talk (15 min)

Bacterial infections pose a serious challenge due to antibiotic resistance; bacteria rapidly adapt to drugs used in clinical practice, resulting in high mortality rates. A deep understanding of the molecular mechanisms by which bacterial pathogens enter host cells provides a foundation for developing new, non-antibiotic strategies to combat these pathogens.
Cell surface is covered with...

2. Semiclassical Simulations of Dissipative Quantum Matter

Dr Viktoria Noel (University of Tübingen)

9/24/26, 2:25 PM

Talk (15 min)

Arrays of individually controlled atoms and ions have emerged as a leading experimental platform for both the exploration of complex quantum matter and the development of quantum technologies. However, guiding these efforts with reliable theoretical predictions is hard: the numerical cost of exact calculations grows exponentially with system size and quickly overwhelms even the largest...

33. Multi-Scale Modeling of Electrochemical Interfaces and Processes

Timo Jacob (Universität Ulm)

9/24/26, 2:40 PM

Talk (15 min)

Batteries, fuel cells, photocells and many other applications are powered by fundamental electrochemical processes. Compared to surface science under UHV conditions, electrochemical systems combine a wide variety of additional effects. These range from the presence of an electrolyte and a multi-component environment to reaction conditions such as finite temperature, pressure, and electrode...

24. Mining Multi-Omics Data for Hidden Mitochondrial Transcripts and Microproteins in Stress-Related Disorders

Sarah Viola Emser (Ulm University)

9/24/26, 3:30 PM

Talk (15 min)

Mitochondria harbor a largely unexplored layer of genetic information beyond the 37 canonical genes currently represented in standard annotations. Recent studies have revealed that an increasing number of non-canonical mitochondrial transcripts and mitochondrial-derived microproteins (MDPs) can act as biologically active molecules involved in cellular stress responses, metabolic regulation,...

21. A standardized workflow for reproducible pig microbiome profiling across laboratories

Samuel Onyilokwu Enokela (Hohenheim Center for Livestock Microbiome Research (HoLMiR), University of Hohenheim)

9/24/26, 3:45 PM

Talk (15 min)

The lack of standardized DNA extraction protocols in pig microbiome research limits reproducibility and cross-study comparability. This challenge becomes even more important in large-scale studies that generate substantial sequencing data and require coordinated, high-throughput computational analysis. To address this, we conducted a large-scale, multi-center validation study across six...

29. How many zones does an electricity market model need?

Thorsten Weiskopf (Karlsruhe Institute of Technology)

9/24/26, 4:00 PM

Talk (15 min)

The geographic scope of a reduced-scope electricity market model, how many zones it represents, and which ones, is a basic design choice. It is also a costly one: data preparation and simulation runtime scale sharply with the number of zones included, and can rise by several orders of magnitude when a full continental model is simulated in place of a single-zone one. Yet how this design choice...

27. Machine-learned intrinsic coordinates for vibrational calculations

Andrey Yachmenev (Stuttgart University)

9/24/26, 4:15 PM

Talk (15 min)

We present a framework for molecular vibrational coordinate optimisation based on generative machine-learning methods, in particular normalising flows.
The computational cost of vibrational configuration interaction (VCI) calculations is largely determined by the size of the correlation space. We show that this space can be substantially reduced by optimising curvilinear coordinates...