I'm a postdoc in the lab of Manu Prakash, supported by a cross-disciplinary fellowship of the Human Frontier Science Program. As joint theorist and experimentalist, I am interested in the physical aspects of ultra-fast biology and hydrodynamic communication between cells (Nature, 2019), mucus clearance in mouse airways (bioRxiv 428573, 2019), 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) since my PhD with Julia Yeomans FRS at the University of Oxford.
Honors & Awards
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)
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
Manu Prakash, Postdoctoral Faculty Sponsor
Collective intercellular communication through ultra-fast hydrodynamic trigger waves.
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
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
Multi-scale spatial heterogeneity enhances particle clearance in airway ciliary arrays
Mucus clearance constitutes the primary defence of the respiratory system against viruses, bacteria and environmental insults. This transport across the entire airway emerges from the integrated activity of thousands of multiciliated cells, each containing hundreds of cilia, which together must coordinate their spatial arrangement, alignment and motility. The mechanisms of fluid transport have been studied extensively at the level of an individual cilium, collectively moving metachronal waves, and more generally the hydrodynamics of active matter. However, the connection between local cilia architecture and the topology of the flows they generate remains largely unexplored. Here, we image the mouse airway from the sub-cellular (nm) to the organ scales (mm), characterising quantitatively its ciliary arrangement and the generated flows. Locally we measure heterogeneity in both cilia organisation and flow structure, but across the trachea fluid transport is coherent. To examine this result, a hydrodynamic model was developed for a systematic exploration of different tissue architectures. Surprisingly, we find that disorder enhances particle clearance, whether it originates from fluctuations, heterogeneity in multiciliated cell arrangement or ciliary misalignment. This resembles elements of "stochastic resonance" in a self-assembled biological system. Taken together, our results shed light on how the microstructure of an active carpet determines its emergent dynamics. Furthermore, this work is also directly applicable to human airway pathologies, which are the third leading cause of deaths worldwide.
Oscillatory surface rheotaxis of swimming E. coli bacteria.
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
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
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
2018; 3 (033103)
View details for DOI 10.1103/PhysRevFluids.3.033103
- Hydrodynamics of micro-swimmers in films JOURNAL OF FLUID MECHANICS 2016; 806: 35-70
Lattice-Boltzmann hydrodynamics of anisotropic active matter
JOURNAL OF CHEMICAL PHYSICS
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
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
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
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 2015; 773: 498-519
- Extended parameterisations for MSTW PDFs and their effect on lepton charge asymmetry from W decays EUROPEAN PHYSICAL JOURNAL C 2013; 73 (2)