Category: Presentation

Invited Talk by G. Volpe at BIST Symposium on Microscopy, Nanoscopy and Imaging Sciences, Castelldefels, 10 March 2023

DeepTrack 2.1 Logo. (Image from DeepTrack 2.1 Project)
AI and deep learning for microscopy
Giovanni Volpe
BIST Symposium on Microscopy, Nanoscopy and Imaging Sciences
Castedefells, 10 March 2023

Video microscopy has a long history of providing insights and breakthroughs for a broad range of disciplines, from physics to biology. Image analysis to extract quantitative information from video microscopy data has traditionally relied on algorithmic approaches, which are often difficult to implement, time consuming, and computationally expensive. Recently, alternative data-driven approaches using deep learning have greatly improved quantitative digital microscopy, potentially offering automatized, accurate, and fast image analysis. However, the combination of deep learning and video microscopy remains underutilized primarily due to the steep learning curve involved in developing custom deep-learning solutions.

To overcome this issue, we have introduced a software, currently at version DeepTrack 2.1, to design, train and validate deep-learning solutions for digital microscopy. We use it to exemplify how deep learning can be employed for a broad range of applications, from particle localization, tracking and characterization to cell counting and classification. Thanks to its user-friendly graphical interface, DeepTrack 2.1 can be easily customized for user-specific applications, and, thanks to its open-source object-oriented programming, it can be easily expanded to add features and functionalities, potentially introducing deep-learning-enhanced video microscopy to a far wider audience.

Presentation by Sreekanth K Manikandan, 10 February 2023

Inferring entropy production in microscopic systems
Sreekanth K. Manikandan
Stanford University
10 February 2023, 15:00, Raven and Fox

An inherent feature of small systems in contact with thermal reservoirs, be it a pollen grain in water, or an active microbe flagellum, is fluctuations. Even with advanced microscopic techniques, distinguishing active, non-equilibrium processes defined by a constant dissipation of energy (entropy production) to the environment from passive, equilibrium processes is a very challenging task and a vastly developing field of research. In this talk, I will present a simple and effective way to infer entropy production in microscopic non-equilibrium systems, from short empirical trajectories [1]. I will also demonstrate how this scheme can be used to spatiotemporally resolve the active nature of cell flickering [2]. Our result is built upon the Thermodynamic Uncertainty Relation (TUR) which relates current fluctuations in non-equilibrium states to the entropy production rate.

References

[1] Inferring entropy production from short experiments [ Phys. Rev. Lett. 124, 120603 (2020) ]

[2] Estimate of entropy generation rate can spatiotemporally resolve the active nature of cell flickering [arXiv:2205.12849]

Bio: Sreekanth completed his PhD at the department of Physics, Stockholm University, in June 2020. His PhD supervisor was Supriya Krishnamurthy. From August 2020 – October 2022, Sreekanth was a Nordita fellow postdoc in the soft condensed matter group at Nordita. Currently, he is a postdoctoral scholar at the Department of Chemistry at Stanford University, funded by the Wallenberg foundation.

Presentation by Natsuko Rivera-Yoshida, 19 January 2023

M. xanthus cell-cell and cell-particle local interactions during cellular aggregation.
Transitions to multicellularity: the physical environment at the microscale
Natsuko Rivera-Yoshida
19 January 2023
16:30, Nexus

Physical environment contribute to both the robustness and the variation of developmental trajectories and, eventually, to the evolutionary transitions. But how? Myxococcus xanthus is a soil bacterium and is widely used as a biological model. In starvation conditions, cells move individually over the substrate into growing groups of cells which, eventually, organize into three-dimensional structures called fruiting bodies. Commonly, this developmental process is studied using standard experimental protocols that employ homogeneous and flat agar substrates, without considering ecologically relevant variables. However M. Xanthus has shown to drastically alter its development when modifying variables such as the substrate topography or stiffness. This modifications occur with trait and scale specificity, at the level of individual cells, large group of cells, fruiting bodies and also at the population scale. We use experimental and analytical tools to study how multicellular organization is altered at different spatial scales and developmental moments.

Presentation by Andreas Menzel, 19 January 2023

Individual and collective motion of nematic, polar, and chiral actively driven objects
Andreas Menzel
19 January 2023
15:30, Nexus

Abstract:
Actively driven objects comprise a manifold of possible different realizations: from self-propelling bacteria and artificial phoretically driven colloidal particles via vibrated hoppers to walking pedestrians. We analyze basic theoretical models to identify generic features of subclasses of such agents. Within this framework, we first address nematic objects [1]. They predominantly propel along one specific axis of their body, but do not feature an explicit head or tail. That is, they can move either way by spontaneous symmetry breaking. This leads to characteristic kinks along their trajectories. Second, we study chiral objects that show persistent bending of their trajectories and migrate in discrete steps [2]. When, additionally, they tend to migrate towards a fixed remote target, rich nonlinear dynamics emerges. It comprises period doubling and chaotic behavior as a function of the tendency of alignment, which is reflected by the trajectories. Third, we consider the collective motion of continuously moving chiral objects in crystal-like arrangements [3]. We here identify a localization transition with increasing chirality or self-shearing phenomena within the crystal-like structures. Overall, we hope by our work to stimulate experimental realization and observation of the various investigated systems and phenomena.

References
[1] A. M. Menzel, J. Chem. Phys. 157, 011102 (2022).
[2] A. M. Menzel, resubmitted.
[3] Z.-F. Huang, A. M. Menzel, H. Löwen, Phys. Rev. Lett. 125, 218002 (2020).

Short Bio:
Andreas Menzel studied physics at the University of Bayreuth (Germany), where he also completed his PhD on the continuum theory of soft elastic liquid-crystalline composite materials. After postdoctoral stays at the University of Illinois at Urbana-Champaign with Prof. Nigel Goldenfeld and at the Max Planck Institute for Polymer Research in Mainz in the department headed by Prof. Kurt Kremer, as well as research stays at Kyoto University with Prof. Takao Ohta, he completed his Habilitation at Heinrich Heine University Düsseldorf at the Theory Institute for Soft Matter headed by Prof. Hartmut Löwen. Amongst others, Andreas is interested in developing and applying explicit Green’s functions methods, statistical descriptions, and continuum theories on soft matter, addressing, for example, functionalized elastic composite materials and active matter. In 2020 he moved as a Heisenberg Fellow of the German Research Foundation to Otto von Guericke University Magdeburg (Germany), where he now heads the department on Theory of Soft Matter / Biophysics.

Invited talk by M. Rey at the University of Granada, 01 December, 2022

Drawing of a coffee mug using only coffee. (Image by M. Rey.)
Marcel Rey got invited to present his recent work on stimuli-responsive emulsions and the coffee ring effect at in the group seminar of the Laboratory of Surface and Interface at the University of Granada.

In the seminar, Marcel Rey talked about his recent advances on understanding the behaviour of stimuli-responsive emulsions and afterwards introduced a simple yet versatile strategy to overcome the coffee ring effect and obtain homogeneous drying of particle dispersions.

Temperature-responsive emulsions combine the long-term stability with controlled on-demand release of the encapsulated liquid. The destabilization has previously been attributed to microgel shrinkage, leading to a lower surface coverage which induces coalescence. We demonstrated that breaking mechanism is fundamentally different than previously thought. Breaking only occurs if the stabilizing soft microgel particles assume a characteristic double-corona microstructure, which serve as weak link enabling stimuli-responsive emulsion behavior. Conversely, emulsions stabilized by regular single-corona microgels remain remarkably insensitive to temperature.

After spilling coffee, a tell-tale circular stain is left by the drying droplet. This universal phenomenon, known as the “coffee ring effect”, is observed independent of the suspended material. We recently developed a simple yet versatile strategy to achieve homogeneous drying of dispersed particles. Modifying the particle surface with surface-active polymers provides enhanced steric stabilization and facilitates adsorption to the liquid/air interface which, after drying, leads to uniform particle deposition. This method is independent of particle size and shape and applicable to a variety of commercial pigment particles promising applications in daily life.

Seminar by G. Volpe at QSIT, ETH Zurich, 3 November 2022

Active droploids. (Image taken from Nat. Commun. 12, 6005 (2021).)
Experimental study of critical fluctuations and critical Casimir forces
Giovanni Volpe
Invited seminar at QSIT/Quantum Center, ETH Zurich
Thursday, November 3, 2022 – 16:00 – 17:00

Critical Casimir forces (CCF) are a powerful tool to control the self-​assembly and complex behavior of microscopic and nanoscopic colloids. While CCF were theoretically predicted in 1978, their first direct experimental evidence was provided only in 2008, using total internal reflection microscopy (TIRM). Since then, these forces have been investigated under various conditions, for example, by varying the properties of the involved surfaces or with moving boundaries. In addition, a number of studies of the phase behavior of colloidal dispersions in a critical mixture indicate critical Casimir forces as candidates for tuning the self-​assembly of nanostructures and quantum dots, while analogous fluctuation-​induced effects have been investigated, for example, at the percolation transition of a chemical sol, in the presence of temperature gradients, and even in granular fluids and active matter. In this presentation, I’ll give an overview of this field with a focus on recent results on the measurement of many-​body forces in critical Casimir forces, the realization of micro-​ and nanoscopic engines powered by critical fluctuations, and the creation of light-​controllable colloidal molecules and active droploids.

Date: Thursday, November 3, 2022
Time: 16:00
Place: ETH Zurich, Campus Hönggerberg, HPF G 6
Host: Lukas Novotny

Presentation by M. Rey at Particle-Based Materials Symposium, Erlangen, 7 October 2022

Drawing of a coffee mug using only coffee. (Image by M. Rey.)
Versatile strategy for homogeneous drying of dispersed particles
Marcel Rey,
Submitted to ISMC 2022
Date: 7 October 2022
Time: 11:20 (CET)

After spilling coffee, a tell-tale stain is left by the drying droplet. This universal phenomenon, known as the “coffee ring effect”, is observed independent of the dispersed material. However, for many technological processes such as coating techniques and ink-jet printing a uniform particle deposition is required and the coffee ring effect is a major drawback.
Here, we present a simple and versatile strategy to achieve homogeneous drying patterns by modifying the surface of the dispersed particles with surface-active polymers. A particle dispersion is mixed with excess surface-active polymers (e.g. polyvinyl alcohol). The polymer partially adsorbs onto the particles and excess polymer is removed by centrifugation and redispersion. While pure particle dispersions form a typical coffee ring, the polymer-modified dispersions dry into a uniform particle deposit. In this talk, I will discuss how the polymer coating prevents accumulation and pinning at the droplet edge and leads to a uniform particle deposition after drying.
It should be highlighted that the presented method is independent of particle shape (e.g. spherical, ellipsoidal or ill-defined particle shapes) and is applicable to a variety of commercial pigment particles (e.g. hematite, goethite or titanium dioxide). Further, the method works for different dispersion media (e.g. aqueous, polar and apolar solvents), demonstrating the practicality of this work for everyday processes.

Presentation by M. Rey at 51st General Assembly of the German Colloid Society, Berlin, 28 September 2022

Drawing of a coffee mug using only coffee. (Image by M. Rey.)
Versatile strategy for homogeneous drying of dispersed particles
Marcel Rey,
Submitted to ISMC 2022
Date: 28 September 2022
Time: 11:20 (CET)

After spilling coffee, a tell-tale stain is left by the drying droplet. This universal phenomenon, known as the “coffee ring effect”, is observed independent of the dispersed material. However, for many technological processes such as coating techniques and ink-jet printing a uniform particle deposition is required and the coffee ring effect is a major drawback.
Here, we present a simple and versatile strategy to achieve homogeneous drying patterns by modifying the surface of the dispersed particles with surface-active polymers. A particle dispersion is mixed with excess surface-active polymers (e.g. polyvinyl alcohol). The polymer partially adsorbs onto the particles and excess polymer is removed by centrifugation and redispersion. While pure particle dispersions form a typical coffee ring, the polymer-modified dispersions dry into a uniform particle deposit. In this talk, I will discuss how the polymer coating prevents accumulation and pinning at the droplet edge and leads to a uniform particle deposition after drying.
It should be highlighted that the presented method is independent of particle shape (e.g. spherical, ellipsoidal or ill-defined particle shapes) and is applicable to a variety of commercial pigment particles (e.g. hematite, goethite or titanium dioxide). Further, the method works for different dispersion media (e.g. aqueous, polar and apolar solvents), demonstrating the practicality of this work for everyday processes.

Invited Talk by G. Volpe at Adaptivity in Nonlinear Dynamical Systems, Potsdam, 23 September 2022

M. xanthus cell-cell and cell-particle local interactions during cellular aggregation.
Feedback between active matter and its environment
Giovanni Volpe
Invited Talk (Online) at the hybrid Workshop: Adaptivity in Nonlinear Dynamical Systems
Potsdam, Germany
23 September 2022, 9:30 CEST

I will present some examples of how feedback cycles can occur between active matter and its environment. In particular, I’ll show the formation of active molecules and active droploids from passive colloidal building blocks; the emergence of non-Boltzmann statistics and active-depletion forces between plates in an active bath; and the environment topography alters the way to multicellularity in the bacterium Myxococcus xanthus.

Presentation by M. Rey at ISMC 2022, Poznan, 23 September 2022

Drawing of a coffee mug using only coffee. (Image by M. Rey.)
Versatile strategy for homogeneous drying of dispersed particles
Marcel Rey, Johannes Walter, Johannes Harrer, Carmen Morcillo Perez, Salvatore Chiera, Sharanya Nair, Maret Ickler, Alesa Fuchs, Mark Michaud, Maximilian J. Uttinger, Andrew B. Schofield, Job H. J. Thijssen, Monica Distaso, Wolfgang Peukert, Nicolas Vogel
Submitted to ISMC 2022
Date: 23 September 2022
Time: 12:10 (CET)

After spilling coffee, a tell-tale stain is left by the drying droplet. This universal phenomenon, known as the “coffee ring effect”, is observed independent of the dispersed material. However, for many technological processes such as coating techniques and ink-jet printing a uniform particle deposition is required and the coffee ring effect is a major drawback.
Here, we present a simple and versatile strategy to achieve homogeneous drying patterns by modifying the surface of the dispersed particles with surface-active polymers. A particle dispersion is mixed with excess surface-active polymers (e.g. polyvinyl alcohol). The polymer partially adsorbs onto the particles and excess polymer is removed by centrifugation and redispersion. While pure particle dispersions form a typical coffee ring, the polymer-modified dispersions dry into a uniform particle deposit. In this talk, I will discuss how the polymer coating prevents accumulation and pinning at the droplet edge and leads to a uniform particle deposition after drying.
It should be highlighted that the presented method is independent of particle shape (e.g. spherical, ellipsoidal or ill-defined particle shapes) and is applicable to a variety of commercial pigment particles (e.g. hematite, goethite or titanium dioxide). Further, the method works for different dispersion media (e.g. aqueous, polar and apolar solvents), demonstrating the practicality of this work for everyday processes.