Harshith Bachimanchi’s half-time seminar. (Photo by Y.-W. Chang.)Harshith Bachimanchi completed the first half of his doctoral studies and defended his half-time on 10th May 2022.
The presentation was held in hybrid format, with part of the audience present in the Nexus room and the rest connected through zoom. The half-time consisted of a presentation of his past and planned projects followed by discussion and questions proposed by his opponent Bernhard Mehlig.
The presentation started with a description of his project about combining holographic microscopy with deep learning to measure the dry mass and three-dimensional swimming patterns of marine microorganisms (Microplankton life histories revealed by holographic microscopy and deep learning). Thereafter, he discussed about some of the new experiments in marine microbial ecology where the technique is currently being used. In the last section, he outlined the proposed continuation of his PhD on studying active matter systems in marine microscopic environments using holographic microscopy and artificial neural networks.
Opponent Bernhard Mehlig (left), Laura Natali (center), and PhD supervisor Giovanni Volpe (right). (Photo by L. Perez.)Laura Natali completed the first half of her doctoral studies and she defended her half-time on the 1st of April 2022.
The presentation was held in hybrid format, with part of the audience in the Von Bahr room and the rest connected through zoom. The half-time consisted in a presentation about her past and planned projects and it was followed by a discussion and questions proposed by her opponent Bernhard Mehlig.
Intercellular communication induces glycolytic synchronization waves between individually oscillating cells
Intercellular communication induces glycolytic synchronization waves between individually oscillating cells Martin Mojica-Benavides, David D. van Niekerk, Mite Mijalkov, Jacky L. Snoep, Bernhard Mehlig, Giovanni Volpe, Caroline B. Adiels & Mattias Goksör
PNAS 118(6), e2010075118 (2021)
doi: 10.1073/pnas.2010075118
arXiv: 1909.05187
Metabolic oscillations in single cells underlie the mechanisms behind cell synchronization and cell-cell communication. For example, glycolytic oscillations mediated by biochemical communication between cells may synchronize the pulsatile insulin secretion by pancreatic tissue, and a link between glycolytic synchronization anomalies and type-2 diabetes has been hypotesized. Cultures of yeast cells have provided an ideal model system to study synchronization and propagation waves of glycolytic oscillations in large populations. However, the mechanism by which synchronization occurs at individual cell-cell level and overcome local chemical concentrations and heterogenic biological clocks, is still an open question because of experimental limitations in sensitive and specific handling of single cells. Here, we show how the coupling of intercellular diffusion with the phase regulation of individual oscillating cells induce glycolytic synchronization waves. We directly measure the single-cell metabolic responses from yeast cells in a microfluidic environment and characterize a discretized cell-cell communication using graph theory. We corroborate our findings with simulations based on a kinetic detailed model for individual yeast cells. These findings can provide insight into the roles cellular synchronization play in biomedical applications, such as insulin secretion regulation at the cellular level.
Neural net with input layer (left), dense internal layers, and output layer (right).
Machine learning for active matter
Frank Cichos, Kristian Gustavsson, Bernhard Mehlig & Giovanni Volpe
Nature Machine Intelligence 2(2), 94–103 (2020)
doi: https://doi.org/10.1038/s42256-020-0146-9
The availability of large datasets has boosted the application of machine learning in many fields and is now starting to shape active-matter research as well. Machine learning techniques have already been successfully applied to active-matter data—for example, deep neural networks to analyse images and track objects, and recurrent nets and random forests to analyse time series. Yet machine learning can also help to disentangle the complexity of biological active matter, helping, for example, to establish a relation between genetic code and emergent bacterial behaviour, to find navigation strategies in complex environments, and to map physical cues to animal behaviours. In this Review, we highlight the current state of the art in the application of machine learning to active matter and discuss opportunities and challenges that are emerging. We also emphasize how active matter and machine learning can work together for mutual benefit.
