NEWS: I'm excited to announce that I will join the faculty as Assistant Professor of Physics & Astronomy at the University of Pennsylvania. Our lab will study biological and soft matter physics. In particular, I'm interested in the collective functionality of intelligent active matter, and how we can bridge multi-scale biology with the physics of solids, fluids and information. If you are interested in joining the Mathijssen lab as a graduate student or postdoc, please get in touch. Apply here:

As joint theorist and experimentalist, I am interested in the physical aspects of ultra-fast biology and hydrodynamic communication between cells (Nature, 2019), pathogen clearance in the airways (Nat Phys, 2020), and bacterial contamination dynamics (Nat Comms, 2019). I also work on the physics of microbial ‘active carpets’ (PRL 2018), interactions between microswimmers and viruses (PRF 2018) and upstream swimming of cells in viscoelastic fluids (PRL 2016).

I completed my PhD with Julia Yeomans FRS at the University of Oxford, and I'm currently a postdoc at Stanford University in the lab of Manu Prakash.

Honors & Awards

  • AFRI Grant, United States Department of Agriculture (USDA) (2020-)
  • Charles Kittel Award, American Physical Society (APS) (2019)
  • International Research Travel Award, American Physical Society (APS) (2019)
  • Cross-disciplinary Fellowship, Human Frontier Science Program (HFSP) (2017-)
  • Sam Edwards PhD Thesis Prize, UK Institute of Physics (IoP) (2016)
  • 30 under 30, Scientific American (2012)
  • Best overall undergraduate, UCL Department of Physics & Astronomy (2012)
  • Faculty Medal, UCL Faculty of Mathematical and Physical Sciences (2012)

Boards, Advisory Committees, Professional Organizations

  • Conference chair, GRS in Jan 2021 about Complex Active and Adaptive Material Systems (2019 - Present)

Professional Education

  • Postdoc, Manu Prakash lab - Stanford University, Bioengineering
  • Doctor of Philosophy, University of Oxford (2016)
  • DPhil thesis, Julia Yeomans FRS - Rudolf Peierls Center for Theoretical Physics, Biophysics
  • Master of Science, University College London (2012)
  • Master thesis, Robert Thorne - MSTW PDF Collaboration, Particle Physics

Stanford Advisors

Lab Affiliations

All Publications

  • Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays NATURE PHYSICS Ramirez-San Juan, G. R., Mathijssen, A. M., He, M., Jan, L., Marshall, W., Prakash, M. 2020
  • Tuning upstream swimming of micro-robots by shape and cargo size Daddi-Moussa-Ider, A., Lisicki, M., Mathijssen, A. J. Physical Review Applied (in press). 2020


    The navigation of micro-robots in complex flow environments is controlled by rheotaxis, the reorientation with respect to flow gradients. Here we demonstrate how payloads can be exploited to enhance the motion against flows. Using fully resolved hydrodynamic simulations, the mechanisms are revealed that allow micro-robots of different shapes to reorient upstream. We find that cargo pullers are the fastest at most flow strengths, but pushers feature a non-trivial optimum as a function of the counter flow strength. Moreover, the rheotactic performance can be maximised by tuning the micro-robot shape or cargo size. These results can be used to control micro-swimmer navigation from first principles, but they also apply to rheotaxis in microbial ecology and the prevention of bacterial contamination dynamics.

    ArXiv link
  • Engineering reconfigurable flow patterns via surface-driven light-controlled active matter Gong, X., Mathijssen, A. J., Bryant, Z., Prakash, M. arXiv. 2020 2004.01368


    Surface-driven flows are ubiquitous in nature, from subcellular cytoplasmic streaming to organ-scale ciliary arrays. Here, we model how confined geometries can be used to engineer complex hydrodynamic patterns driven by activity prescribed solely on the boundary. Specifically, we simulate light-controlled surface-driven active matter, probing the emergent properties of a suspension of active colloids that can bind and unbind pre-patterned surfaces of a closed microchamber, together creating an active carpet. The attached colloids generate large scale flows that in turn can advect detached particles towards the walls. Switching the particle velocities with light, we program the active suspension and demonstrate a rich design space of flow patterns characterised by topological defects. We derive the possible mode structures and use this theory to optimise different microfluidic functions including hydrodynamic compartmentalisation and chaotic mixing. Our results pave the way towards designing and controlling surface-driven active fluids.

  • Towards an analytical description of active microswimmers in clean and in surfactant-covered drops Sprenger, A. R., et al ArXiv 2005.14661. 2020


    Geometric confinements are frequently encountered in the biological world and strongly affect the stability, topology, and transport properties of active suspensions in viscous flow. Based on a far-field analytical model, the low-Reynolds-number locomotion of a self-propelled microswimmer moving inside a clean viscous drop or a drop covered with a homogeneously distributed surfactant, is theoretically examined. The interfacial viscous stresses induced by the surfactant are described by the well-established Boussinesq-Scriven constitutive rheological model. Moreover, the active agent is represented by a force dipole and the resulting fluid-mediated hydrodynamic couplings between the swimmer and the confining drop are investigated. We find that the presence of the surfactant significantly alters the dynamics of the encapsulated swimmer by enhancing its reorientation. Exact solutions for the velocity images for the Stokeslet and dipolar flow singularities inside the drop are introduced and expressed in terms of infinite series of harmonic components. Our results offer useful insights into guiding principles for the control of confined active matter systems and support the objective of utilizing synthetic microswimmers to drive drops for targeted drug delivery applications.

    ArXiv link
  • Collective intercellular communication through ultra-fast hydrodynamic trigger waves. Nature Mathijssen, A. J., Culver, J., Bhamla, M. S., Prakash, M. 2019


    The biophysical relationships between sensors and actuators1-5 have been fundamental to the development of complex life forms. Swimming organisms generate abundant flows that persist in aquatic environments6-13, and responding promptly to external stimuli is key to survival14-19. Here we present the discovery of 'hydrodynamic trigger waves' in cellular communities of the protist Spirostomum ambiguum that propagate-in a manner similar to a chain reaction20-22-hundreds of times faster than their swimming speed. By coiling its cytoskeleton, Spirostomum can contract its long body by 60% within milliseconds23, experiencing accelerations that can reach forces of 14g. We show that a single cellular contraction (the transmitter) generates long-ranged vortex flows at intermediate Reynolds numbers that can, in turn, trigger neighbouring cells (the receivers). To measure the sensitivity to hydrodynamic signals in these receiver cells, we present a high-throughput suction-flow device for probing mechanosensitive ion channels24 by back-calculating the microscopic forces on the cell membrane. We analyse and quantitatively model the ultra-fast hydrodynamic trigger waves in a universal framework of antenna and percolation theory25,26, and reveal a phase transition that requires a critical colony density to sustain collective communication. Our results suggest that this signalling could help to organize cohabiting communities over large distances and influence long-term behaviour through gene expression (comparable to quorum sensing16). In more immediate terms, because contractions release toxins27, synchronized discharges could facilitate the repulsion of large predators or immobilize large prey. We postulate that numerous aquatic organisms other than protists could coordinate their behaviour using variations of hydrodynamic trigger waves.

    View details for DOI 10.1038/s41586-019-1387-9

    View details for PubMedID 31292551

  • Membrane penetration and trapping of an active particle. The Journal of chemical physics Daddi-Moussa-Ider, A., Goh, S., Liebchen, B., Hoell, C., Mathijssen, A. J., Guzman-Lastra, F., Scholz, C., Menzel, A. M., Lowen, H. 2019; 150 (6): 064906


    The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrate through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing us to accurately predict most of our results analytically. This analytical theory helps in identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict the mechanical properties of synthetic minimal membranes.

    View details for PubMedID 30770004

  • Oscillatory surface rheotaxis of swimming E. coli bacteria. Nature communications Mathijssen, A. J., Figueroa-Morales, N., Junot, G., Clément, É., Lindner, A., Zöttl, A. 2019; 10 (1): 3434


    Bacterial contamination of biological channels, catheters or water resources is a major threat to public health, which can be amplified by the ability of bacteria to swim upstream. The mechanisms of this 'rheotaxis', the reorientation with respect to flow gradients, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow using 3D Lagrangian tracking and fluorescent flagellar labelling. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A theoretical analysis explains these rheotaxis regimes and predicts the corresponding critical shear rates. Our results shed light on bacterial transport and reveal strategies for contamination prevention, rheotactic cell sorting, and microswimmer navigation in complex flow environments.

    View details for DOI 10.1038/s41467-019-11360-0

    View details for PubMedID 31366920

  • Nutrient Transport Driven by Microbial Active Carpets. Physical review letters Mathijssen, A. J., Guzmán-Lastra, F., Kaiser, A., Löwen, H. 2018; 121 (24): 248101


    We demonstrate that active carpets of bacteria or self-propelled colloids generate coherent flows towards the substrate, and propose that these currents provide efficient pathways to replenish nutrients that feed back into activity. A full theory is developed in terms of gradients in the active matter density and velocity, and applied to bacterial turbulence, topological defects and clustering. Currents with complex spatiotemporal patterns are obtained, which are tunable through confinement. Our findings show that diversity in carpet architecture is essential to maintain biofunctionality.

    View details for PubMedID 30608743

  • State diagram of a three-sphere microswimmer in a channel. Journal of physics. Condensed matter : an Institute of Physics journal Daddi-Moussa-Ider, A., Lisicki, M., Mathijssen, A. J., Hoell, C., Goh, S., Blawzdziewicz, J., Menzel, A. M., Löwen, H. 2018


    Geometric confinements are frequently encountered in soft matter systems and in particular significantly alter the dynamics of swimming microorganisms in viscous media. Surface-related effects on the motility of microswimmers can lead to important consequences in a large number of biological systems, such as biofilm formation, bacterial adhesion and microbial activity. On the basis of low-Reynolds-number hydrodynamics, we explore the state diagram of a three-sphere microswimmer under channel confinement in a slit geometry and fully characterize the swimming behavior and trajectories for neutral swimmers, puller- and pusher-type swimmers. While pushers always end up trapped at the channel walls, neutral swimmers and pullers may further perform a gliding motion and maintain a stable navigation along the channel. We find that the resulting dynamical system exhibits a supercritical pitchfork bifurcation in which swimming in the mid-plane becomes unstable beyond a transition channel height while two new stable limit cycles or fixed points that are symmetrically disposed with respect to the channel mid-height emerge. Additionally, we show that an accurate description of the averaged swimming velocity and rotation rate in a channel can be captured analytically using the method of hydrodynamic images, provided that the swimmer size is much smaller than the channel height.

    View details for DOI 10.1088/1361-648X/aac470

    View details for PubMedID 29757157

  • Universal entrainment mechanism controls contact times with motile cells PHYSICAL REVIEW FLUIDS Mathijssen, A. J., Jeanneret, R., Polin, M. 2018; 3 (033103)
  • Hydrodynamics of micro-swimmers in films JOURNAL OF FLUID MECHANICS Mathijssen, A. J., Doostmohammadi, A., Yeomans, J. M., Shendruk, T. N. 2016; 806: 35-70
  • Lattice-Boltzmann hydrodynamics of anisotropic active matter JOURNAL OF CHEMICAL PHYSICS de Graaf, J., Menke, H., Mathijssen, A. J., Fabritius, M., Holm, C., Shendruk, T. N. 2016; 144 (13)


    A plethora of active matter models exist that describe the behavior of self-propelled particles (or swimmers), both with and without hydrodynamics. However, there are few studies that consider shape-anisotropic swimmers and include hydrodynamic interactions. Here, we introduce a simple method to simulate self-propelled colloids interacting hydrodynamically in a viscous medium using the lattice-Boltzmann technique. Our model is based on raspberry-type viscous coupling and a force/counter-force formalism, which ensures that the system is force free. We consider several anisotropic shapes and characterize their hydrodynamic multipolar flow field. We demonstrate that shape-anisotropy can lead to the presence of a strong quadrupole and octupole moments, in addition to the principle dipole moment. The ability to simulate and characterize these higher-order moments will prove crucial for understanding the behavior of model swimmers in confining geometries.

    View details for DOI 10.1063/1.4944962

    View details for Web of Science ID 000374527900008

    View details for PubMedID 27059561

  • Hotspots of boundary accumulation: dynamics and statistics of micro-swimmers in flowing films JOURNAL OF THE ROYAL SOCIETY INTERFACE Mathijssen, A. J., Doostmohammadi, A., Yeomans, J. M., Shendruk, T. N. 2016; 13 (115)


    Biological flows over surfaces and interfaces can result in accumulation hotspots or depleted voids of microorganisms in natural environments. Apprehending the mechanisms that lead to such distributions is essential for understanding biofilm initiation. Using a systematic framework, we resolve the dynamics and statistics of swimming microbes within flowing films, considering the impact of confinement through steric and hydrodynamic interactions, flow and motility, along with Brownian and run-tumble fluctuations. Micro-swimmers can be peeled off the solid wall above a critical flow strength. However, the interplay of flow and fluctuations causes organisms to migrate back towards the wall above a secondary critical value. Hence, faster flows may not always be the most efficacious strategy to discourage biofilm initiation. Moreover, we find run-tumble dynamics commonly used by flagellated microbes to be an intrinsically more successful strategy to escape from boundaries than equivalent levels of enhanced Brownian noise in ciliated organisms.

    View details for DOI 10.1098/rsif.2015.0936

    View details for Web of Science ID 000373034300007

    View details for PubMedID 26841796

    View details for PubMedCentralID PMC4780564

  • Upstream Swimming in Microbiological Flows PHYSICAL REVIEW LETTERS Mathijssen, A. J., Shendruk, T. N., Yeomans, J. M., Doostmohammadi, A. 2016; 116 (2)


    Interactions between microorganisms and their complex flowing environments are essential in many biological systems. We develop a model for microswimmer dynamics in non-Newtonian Poiseuille flows. We predict that swimmers in shear-thickening (-thinning) fluids migrate upstream more (less) quickly than in Newtonian fluids and demonstrate that viscoelastic normal stress differences reorient swimmers causing them to migrate upstream at the centerline, in contrast to well-known boundary accumulation in quiescent Newtonian fluids. Based on these observations, we suggest a sorting mechanism to select microbes by swimming speed.

    View details for DOI 10.1103/PhysRevLett.116.028104

    View details for Web of Science ID 000368286300024

    View details for PubMedID 26824571

  • Understanding the onset of oscillatory swimming in microchannels SOFT MATTER de Graaf, J., Mathijssen, A. J., Fabritius, M., Menke, H., Holm, C., Shendruk, T. N. 2016; 12 (21): 4704-4708


    Self-propelled colloids (swimmers) in confining geometries follow trajectories determined by hydrodynamic interactions with the bounding surfaces. However, typically these interactions are ignored or truncated to the lowest order. We demonstrate that higher-order hydrodynamic moments cause rod-like swimmers to follow oscillatory trajectories in quiescent fluid between two parallel plates, using a combination of lattice-Boltzmann simulations and far-field calculations. This behavior occurs even far from the confining walls and does not require lubrication results. We show that a swimmer's hydrodynamic quadrupole moment is crucial to the onset of the oscillatory trajectories. This insight allows us to develop a simple model for the dynamics near the channel center based on these higher hydrodynamic moments, and suggests opportunities for trajectory-based experimental characterization of swimmers' hydrodynamic properties.

    View details for DOI 10.1039/c6sm00939e

    View details for Web of Science ID 000379676800002

    View details for PubMedID 27184912

  • Tracer trajectories and displacement due to a micro-swimmer near a surface JOURNAL OF FLUID MECHANICS Mathijssen, A. J., Pushkin, D. O., Yeomans, J. M. 2015; 773: 498-519
  • Extended parameterisations for MSTW PDFs and their effect on lepton charge asymmetry from W decays EUROPEAN PHYSICAL JOURNAL C Martin, A. D., Mathijssen, A. J., STIRLING, W. J., Thorne, R. S., Watt, B. J., WATT, G. 2013; 73 (2)