Honors & Awards

  • Cross-disciplinary Fellowship, Human Frontier Science Program (HFSP) (2017)
  • Sam Edwards PhD Thesis Prize, UK Institute of Physics (2016)
  • Faculty Medal, UCL Faculty of Mathematical and Physical Sciences (2012)
  • Best overall undergraduate, UCL Department of Physics & Astronomy (2012)

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

  • Oscillatory surface rheotaxis of swimming E. coli bacteria Mathijssen, A. J., Figueroa-Morales, N., Junot, G., Clement, E., Lindner, A., Zoettl, A. Arxiv preprint 1803.01743. 2018


    We demonstrate experimentally and theoretically the existence of oscillatory rheotaxis by E. coli bacteria swimming at surfaces under flow. Three transitions are identified with increasing shear rate: From circular to straight upstream motion, the emergence of oscillations, and finally coexistence of rheotaxis along the positive and negative vorticity directions. We develop a model to explain these transitions and predict the corresponding critical shear rates. Our results shed new light on bacterial transport in the presence of confining walls and strategies for contamination prevention.

  • Self-organised active carpets drive replenishing nutrient currents Mathijssen, A. J., Guzmán-Lastra, F., Kaiser, A., Löwen, H. ArXiv preprint 1804.10271. 2018


    We demonstrate that collective self-organisation in a biofilm or carpet of self-propelled colloids generates coherent solvent currents towards the substrate, and propose that these flows provide efficient pathways to replenish fuel supply or nutrients that feed back into activity. A full theory is developed to express this long-ranged advection in terms of gradients in the active matter density and velocity fields. This approach is applied to bacterial clusters, topological defects of cell orientation, to vortex arrays and turbulent films. Attractive currents with complex spatiotemporal patterns are obtained, which are tuneable by controlling the carpet structure through confinement. This finding shows that diversity in biological and synthetic film architecture is essential to maintain their function.

  • 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)