Robert is a PostDoc in the group of Prof. Carlos Bustamante at the University of California, Berkeley.
During his visit, he will focus on experiments of single-molecule biophysics.
News
Invited talk by Sreekanth K. Manikandan at the online Workshop on Stochastic Thermodynamics (WOST), 14th May 2025
Sreekanth Manikandan
Date: 14 Mar 2025
Time: 17:30 CEST
Place: Online
Part of the Workshop on Stochastic Thermodynamics
Quantifying the spatiotemporal forces, affinities, and dissipative costs of cellular-scale non-equilibrium processes from experimental data and localizing it in space and time remain a significant open challenge. Here, I explore how principles from stochastic thermodynamics, combined with machine learning techniques, offer a promising approach to addressing this issue. I will present preliminary results from experiments on fluctuating cell membranes and simulations of non-equilibrium systems in stationary and time-dependently driven states. These studies reveal potential strategies for localizing entropy production in experimental biophysical contexts while also highlighting key challenges and limitations that must be addressed.
Series of lectures by C. Bustamante, Waernska Professorship lectures, 29 April – 7 May 2025
Professor Carlos Bustamante, who is visiting the Soft Matter Lab between 28 April and 27 May and is a winner of the Waernska Professorship, will be giving a series of lectures on Fundamentals and Applications of Single Molecule Force Spectroscopy.
Professor Carlos Bustamante from UC Berkeley is a pioneer in the use of optical tweezers for the biomechanical study of single molecules. He will explain the basics of how and why you can perform single-molecule experiments with them.
Here is the schedule and location of the lectures:
– 29 April 2025 from 13:00 to 17:00 in Gustaf Dalén-salen;
– 05 May 2025 from 13:00 to 17:00 in FL71;
– 06 May 2025 from 13:00 to 17:00 in Lecture Hall FL71;
– 07 May 2025 from 13:00 to 17:00 in Lecture Hall KB.
Professor Carlos Bustamante, winner of the Waernska Professorship, visits the Soft Matter Lab
Professor Bustamante is a world-renowned expert in single-molecule biophysics and a Full Professor of Molecular and Cell Biology, Chemistry and Physics at the University of California, Berkeley, USA.
His pioneering work has significantly advanced our understanding of the physical behaviour of biological molecules. Using techniques such as optical tweezers, atomic force microscopy and fluorescence microscopy, Professor Bustamante has provided key insights into molecular motors, protein and RNA folding, and the mechanisms of gene expression and regulation.
We are honoured to host Professor Bustamante at the Soft Matter Lab and look forward to exciting scientific exchanges and collaborations during his visit.
His visit is currently planned between 28 April and 27 May 2025.
An additional visit, yet to be confirmed, might take place during the fall of 2025.
Invited talk by L. Viaene at the first PhD Conference at the University of Gothenburg, 25 April 2025
Linde Viaene
Date: 25th of April
Time: 13:00
Place: Veras Gräsmatta, Gothenburg
The importance of protein folding and misfolding is indicated by the broad range of clinical manifestations that have protein aggregation at the base, such as neurodegenerative diseases, cancer and type II diabetes. A key factor in (energy) homeostasis is the DNA configuration of chromatin which allows for essential gene expression and adaptation to environmental factors. The Rpd3 deacetylase histone complex (DHAC) plays a crucial role in gene regulation and its disruption impairs stress-induced gene activation, highlighting its importance in cellular adaptation.
Using Saccharomyces cerevisiae as a model system, we aim to investigate the role of chromatin remodelling components in protein aggregation and cellular rejuvenation, which may influence aggregate retention and recovery speed. We will expose yeast cells to stressors such as heat shock, metabolic shifts, and oxidative stress to assess their effects on protein homeostasis and chromatin regulation. Growth assays will evaluate survival rates, while Western blotting will measure Hsp104 expression, a key heat shock protein involved in aggregate clearance. By employing our bespoke single-molecule fluorescence microscope, we will track aggregate formation, clearance, and spatial localization in live cells at molecular precision.
Our preliminary results indicate that some components of the Rpd3L complex, respectively alter the recovery rate after heat stress exposure. Hence, the goal is to explore further candidate genes and to determine their role in the stress-induced response. By elucidating the role of chromatin remodelers in stress adaptation, our findings may inform novel therapeutic strategies for age-related diseases.
Invited Talk by G. Volpe at OPIC/OMC 2025, Yokohama, Japan, 21 April 2025 (Online, Pre-recorded)
Giovanni Volpe
Optics & Photonics International Congress 2025 (OPIC 2025), The 11th Optical Manipulation and Structured Materials Conference (OMC2025)
Date: 21 April 2025
Time: 13:45 JST
Place: Yokohama, Japan (Online, Pre-recorded)
Yan Chen joins the Soft Matter Lab
Yan received a Ph.D. degree in Materials Physics and Chemistry, Fudan University, China
In her research, she focuses on multistimuli-responsive microrobots.
Invited talk by M. Selin at University of Münster, 11 April 2025
Martin Selin
Date: 11 April 2025
Time: 10:30
Place: University of Münster, Germany
Optical tweezers are powerful tools for probing microscale forces in systems ranging from colloidal particles to single molecules. Here, we demonstrate their use in two different fields. First, by trapping individual colloidal particles, we study their adsorption dynamics at liquid–liquid interfaces, highlighting the critical role of surface chemistry and the presence of polymer shells. We also observe reversible polymer attachments and stretching. Second, we apply tweezers to study single-molecule mechanics. By automating these complex biophysical experiments, we enable high-throughput measurements of molecular dynamics. Our results suggest that, like DNA, synthetic polymers can be effectively described by the worm-like chain model.
BRAPH 2: a flexible, open-source, reproducible, community-oriented, easy-to-use framework for network analyses in neurosciences on bioRxiv
Yu-Wei Chang, Blanca Zufiria-Gerbolés, Pablo Emiliano Gómez-Ruiz, Anna Canal-Garcia, Hang Zhao, Mite Mijalkov, Joana Braga Pereira, Giovanni Volpe
bioRxiv: 10.1101/2025.04.11.648455
As network analyses in neuroscience continue to grow in both complexity and size, flexible methods are urgently needed to provide unbiased, reproducible insights into brain function. BRAPH 2 is a versatile, open-source framework that meets this challenge by offering streamlined workflows for advanced statistical models and deep learning in a community-oriented environment. Through its Genesis compiler, users can build specialized distributions with custom pipelines, ensuring flexibility and scalability across diverse research domains. These powerful capabilities will ensure reproducibility and accelerate discoveries in neuroscience.
Presentation by M. Selin at Ostwald Colloquium, 8 April 2025
Martin Selin
Date: 8 April 2025
Time: 17:40
Place: Center for Interdisciplinary Research, Bielefeld University, Germany
Colloidal particles typically require salt to overcome electrostatic barriers and adsorb to liquid-liquid interfaces. Here, we show that coating particles with polymers enables spontaneous adsorption without salt. Our model system consists of silica cores coated with poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA). Using optical tweezers, we track individual particles showing that the polymer shell makes particles jump into a dodecane–water interface. This behavior extends to other polymers. By tuning pH, we control polymer swelling and adsorption distance. At very low pH, the attachment to the interface is weak enough that the optical tweezers can pull particles out from the interface. During this desorption process we observe single polymers detaching. These findings offer new approaches for designing responsive emulsions.