(Photo by A. Ciarlo.)Janko Vrcek joined the Soft Matter Lab on 9 September 2024.
Janko is a master student in Physics at Chalmers University of Technology.
During his time at the Soft Matter Lab, he will work on Monte Carlo simulations of protein condensates.
Biomolecular condensation is a phenomenon where under certain conditions biological polymers like proteins or RNA segregate out of a solution into a condensate. Many cellular organelles such as nucleolus are considered to be biomolecular condensates. Disruption in the condensation can have serious effects on human health, causing illnesses such as Alzheimer’s disease and cancer. My research investigates conditions for formation of condensates from previously developed theoretical models such as Flory-Huggins theory. We do this by utilizing Monte Carlo simulations of polymer mixtures and comparing results with theoretical models, as well as experimental results.
The three platforms developed to observe and characterise bacterial collective behaviour in different conditions. (Image by J. Dominguez.)Jesús Manuel Antúnez Domínguez defended his PhD thesis on 6 September 2024. Congrats!
The defense took place in PJ, Institutionen för fysik, Origovägen 6b, Göteborg.
Title: Microscopic approaches for bacterial collective behaviour studies.
Abstract: Bacteria significantly impact our lives, from their beneficial role as probiotics to their involvement in infection environments. Their widespread presence is largely due to their ability to adapt to diverse conditions through collective behavior, which enables the development of complex strategies from the contributions of simple individual entities. However the understanding of these systems is limited by the reach of current study techniques. This work presents the development of three platforms designed to perform microscopic studies and characterise bacterial collective behaviors in situ, profiting the advantages of microfluidics over traditional culture techniques.
The first platform integrates bacterial culture on solid agar directly on the microscope stage, allowing for extended observation periods of up to a week. The agar is housed within an elastomer structure sealed with glass, ensuring environmental isolation while maintaining optical accessibility. This platform was used to document the complex social strategies of Myxococcus xanthus, including motility mechanisms, predation organisation, and fruiting body formation.
The second platform is an automated testing system for quantifying bacterial viability under various conditions. Using microfluidic technology, this platform streamlines and parallelise the process. It adapts the Ames genotoxicity test to a miniaturized version, using microscopy imaging as the readout. This approach reduces experimental turnaround time and minimizes the handling of hazardous substances.
The third platform is a microfluidic system designed for the microscopy observation of bacteria within stabilised droplets. This approach enhances throughput and allows for the production of various types of droplets on the same chip. Bacillus subtilis bacteria were encapsulated in these droplets, and their entire biofilm formation life cycle was observed in detail. Parallel to this, custom software was developed specifically for analysing microscopy images to automatically quantify biofilm formation.
Each of these platforms provides a unique perspectives in the study of bacterial collective behavior to offer a comprehensive toolkit for researchers. complementing one another. This work will equip researchers with the tools to address the mysteries of bacterial collective behavior and opens up new possibilities for application and investigation.
Schematic and brightfield image (inset) of the movement of 16μm diameter micromotor under the illumination of linearly polarized 1064nm laser. (Image by G. Wang.)Light-driven metamachines
Gan Wang, Marcel Rey, Antonio Ciarlo, Mohanmmad Mahdi Shanei, Kunli Xiong, Giuseppe Pesce, Mikael Käll and Giovanni Volpe Date: 5 September 2024 Time: 15:45-16:00
The incorporation of Moore’s law into integrated circuits has spurred opportunities for downsizing traditional mechanical components. Despite advancements in single on-chip motors using electrical, optical, and magnetic drives under ~100 μm, creating complex machines with multiple units remains challenging. Here, we developed a ~10 μm on-chip micromotor using a method compatible with complementary metal oxide semiconductors (CMOS) process. The meta-surface is embedded with the motor to control the incident laser beam direction, enabling momentum exchange with light for movement. The rotation direction and speed are adjustable through the meta-surface, along with the intensity and polarization of applied light. By combining these motors and controlling the configuration, we create complex machines with a size similar to traditional machines below 50um, such as the rotary motion mode of multiple gear coupled gear trains, and the linear motion mode combined with rack and pinion, and combine the micro metal The mirror is introduced into the machine to realize the self-controlled scanning function of the laser in a fixed area.
(Photo by A. Ciarlo.)Erik Olsén started his postdoc at the Physics Department of the University of Gothenburg on 26th August 2024. His research is funded by a Swedish research council internation postdoc fellowship with grant nr 2024-00439.
Erik received a PhD degree 2023 in physics from Chalmers University of Technology, Sweden. In his thesis he focused on optical particle characterisation of nanoparticles and submicron particles, with an emphasis on label-free characterisation methods.
The Soft Matter Lab will administrate the postdoc grant while Erik will be in the lab of Sabrina Leslie at University of British Columbia (UBC). At UBC, Erik will combine different image modalities with confined lens induced confinement (CLiC) to characterise different types of biological nanoparticles.
Mirja Granfors with the Best Poster Award at SPIE conference in San Diego. (Photo by G. Volpe.)Mirja Granfors won the best early career researcher poster award at Emerging Topics in Artificial Intelligence (ETAI) 2024 held in San Diego, from 18 to 24 August 2024. The award, consisting of a certificate and a cash prize, is offered by the organizers of the conference, and SPIE Optics + Photonics, and is sponsored by G-Research.
In this poster, Mirja presented her recent work on the development of a graph autoencoder. This graph autoencoder effectively summarizes graph structures while preserving important topological details through multiple hierarchical pooling steps. This enables the extraction of physical parameters describing the graphs. She demonstrated the performance of the graph autoencoder across diverse graph data originating from complicated systems, including the classification of protein assembly structures from single-molecule localization microscopy data, as well as the analysis of collective behavior and correlations between brain connections and age.
Best Poster Award (Image by M. Granfors.)Mirja @ Poster Pops Presentation (Photo by A. Callegari.)Mirja @ Poster Pops Presentation (Photo by A. Callegari.)ETAI Best Poster and Best Presentation Award Ceremony @ SPIE-ETAI. People (left to right): Joana B. Pereira (conference chair), Patrick Grant, Yuzhu Li, Mirja Granfors, Diptabrata Paul. (Photo by G. Volpe.)
One exemplar of the HEXBUGS used in the experiment. (Image by the Authors of the manuscript.)Active Matter Experiments with Toy Robots
Angelo Barona Balda, Aykut Argun, Agnese Callegari, Giovanni Volpe
SPIE-OTOM, San Diego, CA, USA, 18 – 22 August 2024 Date: 22 August 2024 Time: 3:00 PM – 3:15 PM Place: Conv. Ctr. Room 6D
Active matter is based on concepts of nonequilibrium thermodynamics applied to the most diverse disciplines. Active Brownian particles, unlike their passive counterparts, self-propel and give rise to complex behaviors distinctive of active matter. As the field is relatively recent, active matter still lacks curricular inclusion. Here, we propose macroscopic experiments using Hexbugs, a commercial toy robot, demonstrating effects peculiar of active systems, such as the setting into motion of passive objects via active particles, the sorting of active particles based on their mobility and chirality. Additionally, we provide a demonstration of Casimir-like attraction between planar objects mediated by active particles.
