Biological Microswimmers for Cargo Delivery Systems: Modelling, Simulations and Experiments

Project Information

BIOMICAR

Grant agreement ID: 101108868

DOI

10.3030/101108868

Project closed

EC signature date 24 April 2023

Start date 1 January 2024

End date 31 December 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 181 152,96

Coordinated by

UNIVERSIDAD COMPLUTENSE DE MADRID
Spain

Periodic Reporting for period 1 - BIOMICAR (Biological Microswimmers for Cargo Delivery Systems: Modelling, Simulations and Experiments)

Reporting period: 2024-01-01 to 2025-12-31

Summary of the context and overall objectives of the project

Self-propelled microorganisms such as bacteria, protozoa, and microalgae—referred to as biological microswimmers (BM)—play a fundamental role in natural and engineered systems. In nature, their individual and collective dynamics underpin key processes, including the regulation of carbon and oxygen biogeochemical cycles, the structuring of microbial ecosystems, and the emergence of harmful phenomena such as toxin release during phytoplankton blooms under specific environmental conditions. Beyond their ecological relevance, BM have attracted growing interest as functional agents for technological and biomedical applications, particularly as autonomous carriers capable of transporting and releasing microscopic cargoes. A central challenge limiting the translation of these concepts into reliable applications is the lack of precise control over the collective motion of BM. While proof-of-principle studies have demonstrated the feasibility of using BM as transporters, their delivery efficiency remains low. This limitation stems from the intrinsic complexity of real-world environments, where BM swim through confined and porous media, interact with each other and with passive and active agents, and respond to multiple external fields, such as light gradients, chemical cues, and background fluid flows. These factors strongly influence microswimmer trajectories, induce collective behaviors, and significantly reduce the predictability and controllability of their motion.

Current theoretical, computational, and experimental approaches typically address these influences in isolation. To date, the combined and concomitant effects of confinement, external fields, and multi-agent interactions on BM dynamics have not been systematically integrated into simulation frameworks or experimental designs. This fragmentation limits our ability to understand and predict emergent collective behaviors and, critically, to exploit them for targeted transport and delivery. Addressing this gap is essential to advancing both fundamental active-matter science and the conceptual design of efficient BM-based cargo-delivery systems.

The overarching objective of this project is to establish a comprehensive, predictive framework for the collective dynamics of interacting biological microswimmers in complex, confined environments under external stimuli. To achieve this, the project will develop a computational platform capable of simulating suspensions of interacting BM subjected simultaneously to geometric confinement, external fields (such as light, gravity, and chemical gradients), and interactions with other active or passive agents. This platform will enable systematic exploration of how these factors jointly shape collective motion, synchronization, and transport efficiency.

A key element of the project pathway to impact is the tight integration between simulations and experiments. Computational predictions will be continuously tested and refined through microfluidic experiments on suspensions of phototactic microalgae (Chlamydomonas reinhardtii) mixed with passive colloids. This feedback loop will ensure physical realism, validate model assumptions, and accelerate the identification of robust control strategies. By providing quantitative insight into how collective BM behavior can be steered toward desired targets, the project is expected to contribute significantly to the rational design of BM-based delivery systems. At a broader scale, the results will advance the understanding of active matter in realistic environments, with implications for environmental sciences, micro-robotics, and bio-inspired engineering. The anticipated impact spans from improved predictive models of microbial transport in natural porous media to foundational knowledge enabling future applications in targeted delivery and microscale manipulation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Overview of Activities

The project focused on developing theoretical, computational, and experimental approaches to understand and control the collective behavior of biological and model microswimmers in confined environments. The activities were organized around the progressive construction of realistic models of active agents, the implementation of complex confinement geometries, and the comparison of numerical predictions with microfluidic experiments. Particular emphasis was placed on identifying mechanisms that emerge only from the interplay between activity, confinement, and external fields, and on translating these mechanisms into design principles for microscale transport and separation.

Development of Models for Active Agents

A significant activity of the project was the development and improvement of computational models for active agents, including and excluding hydrodynamic interactions depending on the physical question under investigation. Hydrodynamic squirmers were implemented within the Dissipative Particle Dynamics (DPD) framework in LAMMPS, enabling simulations of large suspensions under gravity with complete momentum conservation. In parallel, simplified active particle models, such as run-and-tumble and active Brownian particles without hydrodynamics, were employed to isolate the role of confinement and activity from fluid-mediated effects. This dual modeling strategy allowed systematic disentanglement of the physical mechanisms governing collective behavior.

Modeling of Confinement and External Fields

The project developed flexible numerical implementations of confined environments, including flat walls, asymmetric boundaries, funnel-like obstacles, and microchannel geometries inspired by microfluidic devices. These environments were combined with external fields such as gravity to study sedimentation, accumulation, and transport phenomena. The resulting simulation framework enabled the exploration of realistic scenarios in which microswimmers experience simultaneous confinement, external forcing, and interactions with other active or passive agents.

Gravity-Induced Structuring of Microswimmers

One of the main scientific achievements of the project was the systematic study of squirmer suspensions under gravity. This work culminated in the publication "Sedimentation and structure of squirmer suspensions under gravity" (Soft Matter, 2025). The simulations reproduced known results obtained with alternative numerical techniques, validating the DPD-based squirmer implementation. Beyond validation, the study revealed that the sedimented bottom monolayer transitions to an ordered phase with hexagonal symmetry as the gravitational strength increases. Importantly, the degree of hexagonal order was found to depend on swimmer type, being more robust in pullers than in pushers. These findings provide new insight into gravity and hydrodynamics-driven self-organization in active suspensions and suggest potential routes toward activity-based self-healing or self-organized surfaces.

Conceptual Design of a Separation Microsystem

Another key activity addressed the conceptual design of a microscale separation system exploiting the combined effects of activity and confinement. In "Sorting of binary active–passive mixtures in designed microchannels" (Soft Matter, 2025), mixtures of active and passive particles confined within microchannels with funnel-like obstacles were investigated. The obstacles acted as semipermeable barriers, selectively allowing passive particles to pass through narrow gaps. By tuning the tumbling rate of the active particles and the tilt angle of the obstacles, the system exhibited an optimal regime characterized by maximum separation efficiency and minimal response time. The underlying mechanism was identified as an activity-induced advective drift exerted by active particles on passive particles, leading to effective pumping of passive matter across the channel. This phenomenon, termed active pumping, constitutes a novel and general design principle for microscale separation and transport devices that harness microorganism motility rather than external actuation.

Discovery of Confinement-Induced Collective Motion

A particularly significant and unexpected outcome of the project was the discovery of a new type of collective motion purely induced by confinement. In a study currently under review ("Confinement-induced collective motion in suspensions of run-and-tumble particles", Journal of Chemical Physics), active suspensions were confined in microchannels with asymmetric boundaries: a flat upper wall and a lower wall patterned with funnel-like obstacles that block particle passage. Remarkably, dense traveling bands emerged whose formation and sustained motion required neither explicit alignment interactions, nor shape-induced alignment, nor hydrodynamic interactions, nor the presence of passive particles. The traveling structure was discovered serendipitously during the analysis of simulations originally performed for the separation study. Its propulsion mechanism resembles tracked locomotion observed in heavy vehicles, leading to the designation confinement-induced tracked locomotion. This finding demonstrates that confinement alone can generate coherent, directional collective motion in active matter, opening new perspectives for one-dimensional transport of microscopic objects. The phenomenon is expected to be experimentally realizable using suspensions of Chlamydomonas reinhardtii confined in appropriately designed microfluidic chambers.

Microfluidic Experiments with Microalgae–Colloid Mixtures

Complementing the theoretical and computational work, the project advanced experimental protocols for microfluidic studies of confined mixtures of phototactic microalgae ("Chlamydomonas reinhardtii") and passive colloids. Existing experimental setups were refined to achieve stable confinement, controlled illumination, and reproducible measurements of particle transport. Preliminary results, currently being finalized for publication ("Transport enhancement of colloidal particles in confined microalgal active baths"), demonstrate a significant enhancement of colloidal transport induced by the active bath under confinement. These experiments provide critical validation of simulation predictions and establish a direct link between model active systems and real biological microswimmers.

Summary of Outcomes

Overall, the project delivered a coherent set of models, simulations, and experiments that significantly advance the understanding of active matter under confinement. The outcomes include validated hydrodynamic models, novel confinement-induced ordering and transport mechanisms, and experimentally accessible design principles for microscale separation and delivery systems. Together, these results form a scientific foundation for future developments in active-matter-based technologies.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The project produced a coherent, interlinked set of scientific results that advance understanding of active matter in confined environments and establish new design principles for microscale transport and separation. The main outcomes include: (i) validated computational models for active agents with and without hydrodynamic interactions; (ii) the identification of ordering induced by gravity and hydrodynamics in sedimented active suspensions; (iii) the conceptual design and optimization of microfluidic separation systems exploiting activity and confinement; (iv) the discovery of a previously unreported confinement-induced collective motion; and (v) experimental evidence of transport enhancement in confined active baths of microalgae. Together, these results provide both fundamental insights and a solid basis for future technological developments.

Scientific and technological impacts

From a scientific perspective, the project significantly deepens current knowledge of how confinement, external fields, and activity jointly shape collective behavior in active matter. The demonstration that gravity and hydrodynamics can induce ordered hexagonal monolayers in squirmer suspensions, with a strong dependence on swimmer type, opens new avenues for studying self-organization and phase behavior in active systems. Similarly, the discovery of confinement-induced tracked locomotion reveals that coherent, directional motion can emerge solely from geometric constraints, without alignment interactions or hydrodynamics. This finding challenges existing paradigms in active-matter physics and is expected to stimulate further theoretical and experimental research. From a technological standpoint, the project demonstrates that activity-assisted transport and separation are viable strategies at the microscale. The identification of active pumping as a mechanism for separating passive particles demonstrates how microorganism motility can be harnessed to perform useful work without external actuation. This principle is directly relevant to the conceptual design of cargo delivery systems, lab-on-a-chip devices, and microfluidic sorting platforms, where energy efficiency and design simplicity are critical.

Potential applications and pathways to uptake

While the project primarily focused on fundamental and proof-of-concept studies, the results point toward several application domains. These include targeted delivery and controlled transport of micro-objects, microscale separation and filtration technologies, and the manipulation of colloidal or biological matter in lab-on-a-chip environments. In environmental and biological contexts, the findings may also contribute to improved modeling of microbial transport in porous media and confined natural habitats.
To ensure further uptake and successful translation of the results, several key needs can be identified. First, additional experimental demonstrations are required to validate the proposed mechanisms—such as active pumping and confinement-induced collective motion—using living microswimmers under realistic operating conditions. Scaling studies and robustness analyses will be necessary to assess performance across a broader range of particle types, activities, and geometries. Second, further research is needed to bridge the gap between idealized microfluidic designs and practical devices. This includes integrating more complex boundary conditions, heterogeneous environments, and external controls (e.g. light or chemical gradients) compatible with existing microfabrication techniques. Close collaboration with microfluidics and bioengineering communities will be essential in this phase.

Enablers for exploitation and long-term impact
Although immediate commercialisation was beyond the scope of the project, the results lay the groundwork for future exploitation activities. Support for intellectual property assessment may be required if specific microchannel designs or activity-based transport mechanisms are further developed toward application. Access to dedicated funding for prototype development and demonstration will be a key enabler for progressing from conceptual designs to functional devices. In parallel, engagement with regulatory and standardisation frameworks relevant to microfluidic devices and the use of living microorganisms will be important, particularly for biomedical or environmental applications. Early consideration of biosafety, reproducibility, and controllability will facilitate smoother translation from laboratory research to applied contexts.

In summary, the project delivered a set of high-quality scientific results with clear potential for long-term impact. By uncovering new mechanisms of collective motion and transport induced by activity and confinement, and by linking simulations with experimentally accessible systems, the project contributes foundational knowledge that can underpin future innovations in active-matter-based technologies. Continued research, experimental validation, and targeted support measures will be key to fully realizing the societal and technological benefits of these findings.

Sorting of active-passive mixtures

Confinement-induced collective motion

Squirmers under gravity