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Presentation by M.Selin at S3IC, Barcelona, 23 November 2023

3d Visualization of the full Minitweezers 2.0 system. (Illustration by M. Selin.)
Minitweezers 2.0, Paving the way for fully autonomous optical tweezers experiments.
Martin Selin
Single-Molecule Sensors and NanoSystems International Conference – S3IC 2023
23 November 2023, 11:51 (CET)

Since their invention by Ashkin et al. in the 1980s, optical tweezers have evolved into an indispensable tool in physics, especially in biophysics, with applications spanning from cell sorting to stretching single DNA strands. By the 2000s, commercial systems became available. Nevertheless, owing to their unique requirements, many labs prefer to construct their own, often drawing inspiration from existing designs.

A prominent optical tweezers design is the “miniTweezers” system, pioneered by Bustamante’s group in the late 1990s. This system has been widely adopted globally for force spectroscopy experiments on single molecules, including DNA, proteins, and RNA.

In this presentation, we unveil an advanced iteration of the miniTweezers. By enhancing its control and acquisition capabilities, we’ve augmented its versatility, enabling new experiment types. A significant breakthrough is the integration of real-time image feedback, which paves the way for automated procedures via deep learning-based image analysis, the first of which we demonstrate in this presentation.

We showcase this system’s capabilities through three distinct experiments:

  1. A pulling experiment on a λ-DNA strand. By tethering DNA between two polystyrene beads – one anchored in a micropipette and the other manipulated by the tweezer – we illustrate near-complete automation, with the system autonomously handling bead trapping, attachment of the DNA and the pulling procedure.
  2. An exploration of Coulomb interactions between charged particles. Here, one particle remains in a micropipette, while the other orbits the stationary bead, providing a 3D map of the interaction.
  3. A non-contact stretching experiment on red blood cells is conducted under low osmotic pressure conditions. Modulating the laser power induces cell elongation along the laser’s propagation direction. By correlating this elongation with the optical force exerted by the lasers, we present a simple and non-invasive method to measure membrane rigidity.

In summary, these advancements mark a significant leap in the capabilities and applications of optical tweezers in biophysics. As we push the boundaries of automation and precision, we envision a future where such instruments can unravel even more intricate molecular interactions and cellular mechanics, setting the stage for groundbreaking discoveries.

Presentation by A. Ciarlo at S3IC, Barcelona, 22 November 2023

Illustration of a particle trapped in a two-beam optical trap with transverse offset. (Illustration by A. Ciarlo.)
Intracavity dual-beam optical trap with transverse offset
Antonio Ciarlo
Single-Molecule Sensors and NanoSystems International Conference – S3IC 2023
22 November 2023, 17:04 (CET)

Intracavity optical tweezers are a valuable tool for capturing microparticles in water by exploiting the nonlinear feedback effect induced by particle motion when confined in a laser cavity. This feedback effect arises as a consequence of the particle confinement inside a laser cavity, leading to fluctuations in the optical losses of the cavity due to Brownian motion. Our study extends intracavity optical trapping to both single-beam and counter-propagating dual-beam configurations, allowing us to investigate what happens when the two beams are slightly misaligned.
We used a 1030-nm Yb-doped ring fiber laser (pumped at 976 nm) with a hybrid optical path that allows light propagation in both fiber and air. To switch between single-beam and dual-beam configurations, a free-space removable isolator is incorporated, resulting in a single-beam configuration when the isolator is installed and a dual-beam configuration when the isolator is removed. We tracked particle positions in 3D using digital holographic microscopy and simultaneously measured the powers of the two counter-propagating beams, providing insight into the feedback effect. A crucial aspect of our experiment is the ability to introduce a transverse offset between the two optical beams in the two-beam configuration, resulting in periodic particle motion.
Our study has revealed a periodic orbital rotation of the particle that is closely related to the behavior of the two laser beam powers. We investigated the effect of beam separation and laser pump power on this phenomenon.
This phenomenon results from the interplay of gradient force, scattering force, and nonlinear feedback. The trapped particle undergoes periodic transitions between the two traps, causing a periodic variation in the laser power of the two beams. As a result, the particle acts as a micro-isolator, attenuating the beam in which it is trapped and amplifying the other beam. It was also observed that the duration of the transition increases as the pump power decreases and the distance between the two traps increases.
Future research will focus on refining the trapping configurations to exploit their potential for precise particle manipulation in the field of nanothermodynamics.

Y.-W. Chang received the Gun and Bertil Stohnes Foundation Prize for PhD students

Logo of the Gun and Bertil Stohne’s Foundation. (Image from the Foundation’s website.)

Yu-Wei Chang received one of the Gun and Bertil Stohnes Foundation Prizes for PhD students, with his recent research focusing on deep learning analysis of longitudinal tau pathology. The price consists in 100000 SEK given to one – or shared between two – student(s) at a Swedish university.

The Gun and Bertil Stohnes Foundation awards this prize to research projects in geriatrics that the Board deems of exceptional interest and value.

Anna Canal Garcia, from Karolinska Institutet and supervised by Prof. Joana B. Pereira, is the other recipient of this award. Anna’s research focuses on the intricate multilayer network analysis of brain neuroimaging data.

Environmental Memory Boosts Group Formation of Clueless Individuals published in Nature Communications

Non-monotonic size dependence of group formation on environmental crowding. (Excerpt from Fig. 2 of the manuscript.)
Environmental Memory Boosts Group Formation of Clueless Individuals
Cristóvão S. Dias, Manish Trivedi, Giovanni Volpe, Nuno A. M. Araújo, Giorgio Volpe
Nature Communications, 14, 7324 (2023)
doi: 10.1038/s41467-023-43099-0
arXiv: 2306.00516

The formation of groups of interacting individuals improves performance and fitness in many decentralised systems, from micro-organisms to social insects, from robotic swarms to artificial intelligence algorithms. Often, group formation and high-level coordination in these systems emerge from individuals with limited information-processing capabilities implementing low-level rules of communication to signal to each other. Here, we show that, even in a community of clueless individuals incapable of processing information and communicating, a dynamic environment can coordinate group formation by transiently storing memory of the earlier passage of individuals. Our results identify a new mechanism of indirect coordination via shared memory that is primarily promoted and reinforced by dynamic environmental factors, thus overshadowing the need for any form of explicit signalling between individuals. We expect this pathway to group formation to be relevant for understanding and controlling self-organisation and collective decision making in both living and artificial active matter in real-life environments.

Yu-Wei Chang presented his half-time seminar on 3 November 2023

Opponent Saikat Chatterjee (on Zoom), Yu-Wei Chang (left), and PhD co-supervisor Joana B. Pereira (right). (Photo by P.-J. Chien.)
Yu-Wei Chang completed the first half of his doctoral studies and he defended his half-time on the 3rd of November 2023.

The presentation was conducted in a hybrid format, with part of the audience present in the Nexus room and the remainder connected through Zoom. The seminar comprised a presentation covering both his completed and planned projects, followed by a discussion and questions posed by his opponent, Prof. Saikat Chatterjee.

The presentation commenced with an overview of his concluded projects. The first project involves handling incomplete medical datasets using neural networks and is published in ‘Machine Learning: Science and Technology.‘ It then transitioned to his second project, focusing on the development of software for brain connectivity analysis using multilayer graphs and deep learning. The corresponding repository is accessible on GitHub. In the final segment, he outlined the proposed continuation of his PhD, discussing an ongoing project centered around the deep learning analysis of longitudinal brain neural imaging data.

Laura Pérez García defended her PhD thesis on 12 October 2023. Congrats!

A dielectric particle under the influence of the gradient and scattering force. (Image by L. Pérez García.)
Laura Pérez  García defended her PhD thesis on the 12th of October at 13:15. Congrats!
The defense took place in Faraday, Institutionen för fysik, Origovägen 6b, Göteborg.

Title: Advanced methods for the calibration of optical tweezers

Abstract: Optical tweezers have enabled the manipulation of micron-sized particles with great accuracy since their invention by Arthur Ashkin and colleagues in the 1980s. This technique has had an impact in multiple areas, including biology, physics, nanotechnology, spectroscopy, soft matter and nanothermodynamics.
To perform experiments requiring quantitative transduction
of forces with optical tweezers, the optical tweezers need to be calibrated; that is their stiffness needs to be determined. In this thesis, I present the results that I have obtained for the calibration of optical tweezers using probabilistic approaches.
The goal of these approaches is to use the available data most efficiently and even be able to have an estimation of the error associated with the calibration. This is of the utmost importance when one has limited data, as is often the case with systems out of equilibrium, low signal-to-noise ratios, and systems in which the conditions change with time quite fast. This thesis is divided into two problems. The first problem I had was the unavailability of a comprehensive method to measure force fields in extended, non-conservative, and unstable equilibrium points. For this problem I used Bayesian inference in the form of a maximum likelihood estimator, which allowed me to characterize the force field even in conditions previously not possible to tackle. This parameter-free method called FORMA proved to be more precise, accurate, faster, and less data-intensive than the previous conventional method, i.e. equipartition, MSD, ACF, and PSF. Not only that, but it allowed me to characterize the force field generated by Laguerre-Gaussian beams with different orbital/spin angular momentum, a double-well potential, and a speckle pattern.
The second problem I tackled was the error in the estimators due to
limited bandwidth and finite integration time. For this, we developed the joint probability density function of observing the particle at a given set of positions and times. We derived generalized formulas for the calibration methods; these new formulas successfully correct for the overestimation of the stiffness and the underestimation of the diffusion coefficient caused by a finite integration time; it also accounts for the limited sampling frequency and the trajectory length.
In general, this thesis shows the potential of having a probabilistic and inference approach to the problem of deducing the set of parameters that characterize the Langevin equation of motion of a particle from a time series of its position. The solution to this problem has applications not only to the calibration of optical tweezers but also to microrheology, the behavior of single molecules inside a cell, and animal migration.

Thesis: https://hdl.handle.net/2077/78214

Supervisor: Giovanni Volpe
Examiner: Mattias Goksör
Opponent: Balpreet Singh Ahluwalia
Committee: Thomas Huser, Juliane Simmchen, Kirstine Berg-Sørensen
Alternate board member: Mattias Marklund

Presentation by E. Erdem, 4 October 2023

Schematic of a red blood cell in a focused optical beam. (Image by E. Erdem.)
Optical trapping of red blood cells and different geometrical shapes
Emir Erdem

Red Blood Cells (RBC), also known as erythrocyts, are essential cells that are present in the blood of every vertebrate. Because of their hemoglobin protein content, they carry oxygen to the cells and perform a vital function. Due to their complex shapes, behavior of cells like RBCs under optical forces are not fully been discovered. In this study, the behavior of RBCs as well as other shapes under optical trap are simulated using OTGO which is a numeric toolbox utilizing geometrical optics approximation for optical calculations. As a result of the simulations, it is observed that the RBC aligns itself in a vertical configuration, parallel to the incident beam propagating towards the cell from below. Conducted static analysis showed that it is possible to stably trap a RBC in all three dimensions. The center of the trap is near the edge of the cell, where the thickness is larger. After the analysis on RBC, how well different geometrical shapes can optically be trapped are investigated by integrating different shapes modeled by spherical harmonics to OTGO. A similar static analysis is conducted on a dumbbell shape and its trapping effectiveness is compared with an ellipsoid. A dumbbell shape can effectively be trapped in the horizontal plane similar to an ellipsoid, but in the light propagation direction, it is more challenging to trap the shape and it requires modifications on optical properties of the setup. The aim of this study after this point is to optimize the optical force calculations by training a neural network model and to apply flow conditions to cells.

Giovanni Volpe awarded the Faculty of Science’s 2023 Research Award

(Image adapted from here.)
Giovanni Volpe received the Faculty of Science’s 2023 Research Award for using methods from physics to look into complex and biological systems.

The Research Award of the Faculty of Science of the University of Gothenburg recognizes development of a research specialization that significantly contributes to novelty in the faculty’s research. The award recipient receives a diploma and a research grant of SEK 250,000. This year, the award ceremony will be held on 19 October.

A short interview with Giovanni Volpe regarding this achievement can be found at the link: Giovanni Volpe awarded the Faculty of Science’s 2023 Research Award.

Alfred Bergsten defended his Master Thesis on 18 September 2023. Congrats!

Trajectory of a hexagonal cluster formed by a transparent particle (blu circle) and six light-absorbing particles (red circles) in a traveling sinusoidal optical pattern, in the absence of thermal noise. The direction of the motion of the optical pattern is given by the arrow. The trajectory’s duration is 30 s. (Image by A. Bergsten.)
Alfred Bergsten defended his Master Thesis on 18 September 2023 at 17:00. Congrats!

Title: Controlling Active Clusters Using Wave-Shaped Light Patterns

Abstract:
Colloidal systems appear in various contexts. In some of these systems, thermophoretic forces can arise around otherwise passive particles when they are illuminated, leading to the emergence of complex behaviours. These types of systems has been extensively studied under constant, uniform light where the emergent behaviours are simply activated and deactivated. The aim of this project is to show that the emergent behaviour can not only be activated and deactivated, but also controlled by employing more complex light patterns.
The model used in this project includes Brownian motion and thermophoretic forces, with collisions between particles being resolved by a volume exclusion method. The thermophoretic forces are activated by employing travelling wave light patterns to affect the behaviours of different clusters formed as a result of these forces. Two different patterns are then superimposed to show that more complex light patterns can induce more complex behaviours.
This study is mostly qualitative in nature and only conducted in simulations. While the parameter space has only been roughly explored and the study needs to be validated through physical experiments, the results of the project indicate that a more comprehensive exploration of the parameter space for a broader range of clusters can be of interest.

Supervisor: Agnese Callegari
Examiner: Giovanni Volpe
Opponent: Simon Carlson

Place: Nexus
Time: 18 September, 2023, 17:00

Presentation by H. Bachimanchi at International Forum for Computer vision in Ecology and Evolution, Lund University, 21 September 2023

Planktons imaged under a holographic microscope. (Illustration by J. Heuschele.)

Bringing microplankton to focus: Holography and deep learning
Harshith Bachimanchi
21 September 2023, 11:15 AM CEST

The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.

The article related to this presentation can be found at the following link: Microplankton life histories revealed by holographic microscopy and deep learning.

The recorded presentation can be found here: