Presentation – Page 10 – Soft Matter Lab

Invited Talk by G. Volpe at UCLA, 19 August 2022

Quantitative Digital Microscopy with Deep Learning
Giovanni Volpe
19 August 2022, 14:40 (PDT)
At the intersection of Photonics, Neuroscience, and AI
Ozcan Lab, UCLA, 19 August 2022

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 Murat Nurati Yesibolati, 4 August 2022

Measuring translational and rotational dynamics of colloid nanoparticles at the nanoscale with liquid-phase transmission electron microscopy
Murat Nulati Yesibolati, Assistant professor, Technical University of Denmark
4 August 2022, 10:30 CEST

How nanoparticles (NPs) in a liquid suspension grow, transport, and interact with each other and surrounding interfaces are of fundamental interest in the colloidal matter, biomedical applications, microfluidics, and artificial micro/nanoscopic motors. Traditionally, imaging of such liquid processes has been limited to optical microscopy (OM). Bulk-level methods such as conventional OM and light scattering methods such as dynamic light scattering (DLS) cannot deliver nanometer spatial resolution at the single-particle level. Recently, liquid-phase transmission electron microscopy (LPTEM) [1] has revolutionized the access to the nanoscale, label-free imaging of a wide variety of liquid processes. Typically, the liquid cells used for LPTEM consist of electron-transparent silicon nitride (SiNx) windows suspended on two Si chips, which enclose a liquid sample layer with a thickness ranging from a few hundred nanometers to a couple of microns. With LPTEM, NP dynamics, such as nucleation and growth, self-assembly, and interactions, have been studied with sub-nanometer spatial resolution and millisecond temporal resolution.
We demonstrate how LPTEM can be used to measure the motion of individual NPs and agglomerates. Only at low electron flux do we find that individual NPs exhibit Brownian motion consistent with optical control experiments and theoretical predictions for unhindered passive diffusive motion in bulk liquids [2]. For increasing electron flux, we find increasingly faster than passive motion that still appears effectively Brownian. We discuss the possible origins of this beam–sample interaction. This establishes conditions for the use of LPTEM as a reliable tool for imaging nanoscale hydrodynamics at the nanoscale.

Bio
Murat N. Yesibolati is an Assistant Professor at Technical University of Denmark (DTU), Denmark. Murat defended his Ph.D. thesis titled “Electron holography and particle dynamics in liquid phase transmission electron microscopy” at DTU in 06.2018 under the supervision of Prof. Kristian Mølhave, DTU. Currently, he is focusing on developing a novel nanochannel liquid cell and exploring mass transport in nanochannels using advanced transmission electron microscopy. His research was supported by the Technical University of Denmark, by the Danish Research Council for Technology, grant no. 12-126194, the Advanced Materials for Energy-Water Systems (AMEWS) Center, Office of Science, Basic Energy Sciences, USA, grant number DE-AC02-06CH11357, and the VILLUM foundation, grant number 00028273.

References
[1] de Jonge, N. and F.M. Ross, Electron microscopy of specimens in liquid. Nature Nanotechnology, 2011. 6: p. 695.
[2] Yesibolati, M.N., et al., Unhindered Brownian Motion of Individual Nanoparticles in Liquid-Phase Scanning Transmission Electron Microscopy. Nano Letters, 2020. 20(10): p. 7108-7115.

Place: Nexus
Date: 4 August 2022
Time: 10:30 CEST

Invited Talk by G. Volpe at Nordita, Stockholm, 2 August 2022

Interplay between active particles and their environment
Giovanni Volpe
2 August 2022, 10:30 (CEST)
Nordita workshop: Current and Future Themes in Soft and Biological Active Matter
Albano Building 3
Stockholm, 25 July-19 August 2022

In this seminar, I will present some examples of how the behaviour of active particles can be influenced by their 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.

Invited Talk by G. Volpe at MoLE Conference 2022, Donostia/San Sebastián, Spain, 27 July 2022

Artificial intelligence in microscopy, photonics, and active matter
Giovanni Volpe
27 July 2022, 12:40 (CEST)
MoLE Conference 2022
Donostia/San Sebastián, Spain, 25-29 July 2022

After a brief overview of artificial intelligence, machine learning and deep learning, I will present a series of recent works in which we have employed deep learning for applications in microscopy, optical tweezers, and active matter. In particular, I will explain how we employed deep learning to enhance digital video microscopy, to perform virtual staining of tissues, to estimate the properties of anomalous diffusion, to characterize microscopic force fields, to improve the calculation of optical forces, and to characterize nanoparticles. Finally, I will provide an outlook on the future for the application of deep learning in these fields.

Invited Talk by G. Volpe at Active and Intelligent Living Matter Conference, Erice, 30 June 2022

Artificial intelligence in microscopy, photonics, and active matter
Giovanni Volpe
30 June 2022, 16:20 (CEST)
Active and Intelligent Living Matter Conference
Erice, Italy, 26 June-1 July 2022

Presentation by Vide Ramsten, 10 June 2022

Observer, Target Generation and Control Design in Robotics
Vide Ramsten
10 June 2022, 15:00 CET

Abstract
In this presentation, three topics related to Control Theory will be discussed together with practical examples from my Bachelor and Master thesis projects. First, the concept of state observers will be presented, where internal system states are estimated based on the measurable outputs of the system. Second, target generation will be discussed, in which the particular output or state trajectory of the system that is desired, is created. Lastly, we consider controller design, where we specify how to create the input given the previously defined parts such as target reference, measurable output and estimated system states. The theory will be applied to two projects. One in which a wheeled robot is developed for guiding purposes, so that the robot can show users the way to certain locations specified by the user. The project gives examples of state observers by localization algorithms, as well as target generation by path planning algorithms. The other example is a robotic testing system for passive prosthesis, where target generation through a motion-capture system is used as a reference for robot motion. A control strategy has been implemented in order to track this reference signal.

Short Bio
Vide Ramsten got his Bachelor degree in Automation and Mechatronic at the Chalmers University of Technology. After that, he continued his studies in a master programme in Systems, Control and Mechatronics at Chalmers. During his master, he did a double degree exchange with the University of Stuttgart, Germany in Engineering Cybernetics. While in Germany, he did a six-month internship at the robotics company BEC Gmbh focused on applications of control in robotics, as well as his master thesis at the Fraunhofer Institute of Manufacturing Engineering and Automation IPA.

Date: 10 June 2022
Time: 11:00
Place: Faraday

Invited Talk by G. Volpe at International Workshop On Active Systems, IIT Madras, India, 9 June 2022.

Emergent Complex Behaviors in Active Matter
Giovanni Volpe
9 June 2022, 14:30 (IST)
Online for MNBF Workshop: International Workshop On Active Systems
IIT Madras, India, 8-9 June 2022

Presentation by Lun Li, 7 June 2022

Robots in real-world scenarios
Lun Li
7 June 2022, 15:00 CET

Abstract
In this presentation, I will demonstrate how robots can work in the real-world and dynamic environments assisting or replacing humans and present examples from my previous work experiences. I will also explain the basic knowledge about robots, the challenges to design a robust robot system for business, and the current state of the robotics industry.

Short Bio
Lun Li is a robotics engineer. His work focuses on artificial intelligence and robot designing in the areas of robot navigation, manipulation, and cooperation. In the past three years, he has served as the CTO of robot startups in China. He has led two robot projects, one is an agricultural robotic jasmine tea harvester, and the other is an industrial unmanned forklift. The latter has been successfully launched in the market. Before entering the workplace, he got his two bachelor’s degrees from Beihang University in China and a master’s degree from Texas A&M University in United States.

Date: 7 June 2022
Time: 15:00
Place: Faraday

Presentation by R. Biswas, 1 June 2022

Investigating the micro-rheology of an aging colloidal clay suspension using an optical tweezer
Rajkumar Biswas
Raman Research Institute, Bangalore, India.
1 June 2022, 12:30 CET

Optical tweezers (OT) can be employed to measure pico-Newton forces acting on a colloidal particle trapped in a medium and have been used to successfully probe complex systems having fragile structures. In this work, we use an optical tweezer setup to study aging aqueous suspensions of Laponite clay particles of different concentrations. Laponite particles in aqueous suspension form fragile networks whose rigidities grow with time due to the gradual evolution of inter-particle electrostatic interactions. Using OT, we study the displacements of a trapped micron-sized colloidal bead in a Laponite suspension medium during the evolution of the underlying structures. By analyzing the power spectrum, we demonstrate that the viscosity of the aging Laponite suspension increases with time. Furthermore, we perform active micro-rheology experiments wherein we apply a sinusoidal oscillation to the sample cell while keeping the particle trapped in the Laponite suspension. Simultaneously, the force response of the trapped particle is recorded during the controlled applied oscillation. The phase lag between the applied oscillatory signal and the force experienced by the trapped particle due to the oscillatory deformation is calculated. A range of frequencies is applied to estimate the elastic (G’) and viscous (G”) moduli of the Laponite suspension over a broad range of time scales and at different suspension ages. It is found that G’ is lower than G” at the lower frequencies and eventually crosses G” at a frequency that depends on the Laponite concentration. We change the size of the trapped particle to study how the probe particle size affects the micro-rheological measurements of the viscoelastic gel-like medium. We next investigate the concentration- and aging-dependences of the fragile structures in Laponite suspensions of different concentrations using cryogenic electron microscopy. The average pore areas of these structures are seen to decrease with increasing Laponite concentrations. We show that the crossover frequency of G’ and G”, obtained from micro-rheological measurements, is proportional to the average diameter of the pores in the Laponite gel measured using electron microscopy.

Short Bio
Rajkumar Biswas is currently doing his PhD in Raman Research Institute (RRI), India. Before joining RRI in 2016, he completed his bachelor’s and masters in Physics from St. Xavier’s college, Kolkata and Indian Institute of Technology, Guwahati (IITG) respectively. In RRI he is working in the Soft Condensed Matter group with Prof. Ranjini Bandyopadhyay. His research focuses on rheological and dynamical properties of different soft matter systems. He has worked on various projects which includes rheological studies of Laponite gels using falling ball viscometer and optical tweezer. Along with that, he has been studying the dynamical heterogeneities in colloidal and granular systems.

Seminar by Eric Clément, 31 May 2022

Slide from E. Clément’s presentation. *(Image by A. Callegari via Zoom)*

Bacteria exploring Newtonian and non-Newtonian complex fluids: from behavioral variability to medium assisted tumbling
Eric Clément
PMMH-ESPCI-PSL, Sorbonne University, University Paris-Cité
31 May 2022, 11:00 CET

Understanding the way motile micro-organisms such as bacteria explore their environment is central to many ecological, medical and biotechnological questions. Here, I will present recent advances on the actual spatial exploration process undertaken by flagellated bacteria such as E.coli, undergoing sequences of runs and tumbles, leading to a random-walk. The extreme sensitivity of the motor rotation switch (CCW/CW) to the presence of a phosphorylated protein (CheYP) in its vicinity, leads to a behavioral variability of run-times, characterized by a log-normal distribution [1]. This mechanism prevails in most Newtonian fluids and has important consequences on the residence times at surfaces [2] as well as the large scale transport and dispersion in confined environments [3]. However when the surrounding fluid is a yield-stress fluid, the locally high resistance to penetration takes control of the exploration process and the run persistence time distribution is strongly affected by the mechanical bending of the flagella bundle, hence controlling the spatial diffusivity as well as the onset of a motility barrier.

[1] N. Figueroa-Morales et al., 3D spatial exploration by E.coli echoes motor temporal variability, Phys. Rev. X, 10, 021004 (2020).
[2] G. Junot et al., Run-to-tumble variability controls the surface residence times of E. coli bacteria, to appear in Phys. Rev. Lett. (2022).
[3] N. Figueroa-Morales et al., E.coli “super-contaminates” narrow channels fostered by broad motor switching statistics, Science Advances, 6, eaay0155 (2020).