From collective motion to single particle trajectory segmentation : Insights into particle dynamics at the microscopic scale
(2025)- Abstract
- The study of physical systems at the microscopic scale often reveals emergent behaviors driven by thermal fluctuations and interactions. The characterization of such systems permits a deeper understanding of how these driving forces give rise to collective phenomena and functional responses. This thesis investigates two classes of microscopic systems: momentum-conserving active matter, or so-called "wet" active matter, where the constituents have the ability to transform energy into motion and interact through hydrodynamic interactions; and passive Brownian particles, where diffusion is transient due to thermal fluctuations and molecular interactions.
In wet active matter, interactions between active stresses and fluid flows lead... (More) - The study of physical systems at the microscopic scale often reveals emergent behaviors driven by thermal fluctuations and interactions. The characterization of such systems permits a deeper understanding of how these driving forces give rise to collective phenomena and functional responses. This thesis investigates two classes of microscopic systems: momentum-conserving active matter, or so-called "wet" active matter, where the constituents have the ability to transform energy into motion and interact through hydrodynamic interactions; and passive Brownian particles, where diffusion is transient due to thermal fluctuations and molecular interactions.
In wet active matter, interactions between active stresses and fluid flows lead to complex spatiotemporal dynamics that differ from those in dry active systems. While giant number fluctuations (GNFs), characterized by superlinear scaling of density fluctuations with system size, are a feature of dry active matter with long-range orientational order, theoretical analyses suggest that long-range nematic order is unstable in wet active matter due to hydrodynamic instabilities at finite wavelengths. Consequently, the mechanism responsible for GNFs in dry systems may not operate at large scales in wet active systems. Using large-scale lattice Boltzmann simulations of dilute suspensions of pusher-type microswimmers in three-dimensional unbounded fluids, this work demonstrates that enhanced, super-Gaussian number fluctuations emerge above the transition to collective motion. However, these fluctuations are confined to length scales comparable to the swimmers’ persistence length, which also sets the typical size of transient nematic domains. At larger scales, number fluctuations return to Gaussian statistics. We also address the role of dimensionality by investigating two-dimensional microswimmer suspensions, our results show that the transition is almost completely smoothened out for small to intermediate values of the persistence length. Furthermore, for large values of the persistence length , we observe a discontinuous transition to a characteristic, stationary state with extensile flow structures spanning the whole system.
The second project addresses passive Brownian particles switching between diffusive states, typical in molecular binding or conformational changes. A computationally efficient segmentation method combines Gaussian filtering of displacement time series with Gaussian mixture models to classify states. Tests on synthetic two-state trajectories show high accuracy across diffusion constants and lifetimes, with robustness to motion blur and localization noise. This approach offers a transparent, lightweight alternative for real-time single-particle tracking analysis. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/b5a37d26-14a6-41e9-a68a-769614230a21
- author
- El Korde, Ismail LU
- supervisor
- opponent
-
- Professor Pagonabarraga, Ignacio, Universitat de Barcelona
- organization
- publishing date
- 2025
- type
- Thesis
- publication status
- published
- subject
- keywords
- Active Matter, Single particle tracking, collective motion
- pages
- 123 pages
- publisher
- Lund
- defense location
- Kemicentrum, KC:A
- defense date
- 2025-12-11 13:00:00
- ISBN
- 978-91-8096-138-7
- 978-91-8096-139-4
- language
- English
- LU publication?
- yes
- id
- b5a37d26-14a6-41e9-a68a-769614230a21
- date added to LUP
- 2025-11-14 14:05:47
- date last changed
- 2025-11-18 09:45:03
@phdthesis{b5a37d26-14a6-41e9-a68a-769614230a21,
abstract = {{The study of physical systems at the microscopic scale often reveals emergent behaviors driven by thermal fluctuations and interactions. The characterization of such systems permits a deeper understanding of how these driving forces give rise to collective phenomena and functional responses. This thesis investigates two classes of microscopic systems: momentum-conserving active matter, or so-called "wet" active matter, where the constituents have the ability to transform energy into motion and interact through hydrodynamic interactions; and passive Brownian particles, where diffusion is transient due to thermal fluctuations and molecular interactions.<br/><br/>In wet active matter, interactions between active stresses and fluid flows lead to complex spatiotemporal dynamics that differ from those in dry active systems. While giant number fluctuations (GNFs), characterized by superlinear scaling of density fluctuations with system size, are a feature of dry active matter with long-range orientational order, theoretical analyses suggest that long-range nematic order is unstable in wet active matter due to hydrodynamic instabilities at finite wavelengths. Consequently, the mechanism responsible for GNFs in dry systems may not operate at large scales in wet active systems. Using large-scale lattice Boltzmann simulations of dilute suspensions of pusher-type microswimmers in three-dimensional unbounded fluids, this work demonstrates that enhanced, super-Gaussian number fluctuations emerge above the transition to collective motion. However, these fluctuations are confined to length scales comparable to the swimmers’ persistence length, which also sets the typical size of transient nematic domains. At larger scales, number fluctuations return to Gaussian statistics. We also address the role of dimensionality by investigating two-dimensional microswimmer suspensions, our results show that the transition is almost completely smoothened out for small to intermediate values of the persistence length. Furthermore, for large values of the persistence length , we observe a discontinuous transition to a characteristic, stationary state with extensile flow structures spanning the whole system.<br/><br/>The second project addresses passive Brownian particles switching between diffusive states, typical in molecular binding or conformational changes. A computationally efficient segmentation method combines Gaussian filtering of displacement time series with Gaussian mixture models to classify states. Tests on synthetic two-state trajectories show high accuracy across diffusion constants and lifetimes, with robustness to motion blur and localization noise. This approach offers a transparent, lightweight alternative for real-time single-particle tracking analysis.}},
author = {{El Korde, Ismail}},
isbn = {{978-91-8096-138-7}},
keywords = {{Active Matter; Single particle tracking; collective motion}},
language = {{eng}},
publisher = {{Lund}},
school = {{Lund University}},
title = {{From collective motion to single particle trajectory segmentation : Insights into particle dynamics at the microscopic scale}},
url = {{https://lup.lub.lu.se/search/files/233005143/Ismail_El_Korde_-_WEBB.pdf}},
year = {{2025}},
}