Jonasz Słomka

LaTeX: Jonasz S\l{}omka

ETH Zürich
Institute of Environmental Engineering
Laura-Hezner-Weg 7, HIF D22.1
8093 Zürich

email: jslomka "at"

I am a junior group leader (SNF Ambizione Fellow) at the Institute of Environmental Engineering at ETH Zürich. Previously, I was a post-doctoral fellow at ETH Zürich with Roman Stocker, and before that, I completed my PhD in Physical Applied Mathematics at MIT with Jörn Dunkel.

We are interested in BioEncounters - encounters between microorganisms in space and time. By combining experimental, computational and mathematical approaches, we aim to quantify how BioEncounters mediate microbial interactions.

Short bio (click here for my full CV):

  • since 2021, Junior Group Leader (SNF Ambizione Fellow), ETH Zürich, Switzerland
  • 2018 - 2021, ETH Postdoctoral Fellow, ETH Zürich, Switzerland
  • 2013 - 2018, PhD in Physical Applied Mathematics, Massachusetts Institute of Technology, USA
  • 2012 - 2013, Master of Advanced Study in Mathematics (Part III), University of Cambridge, UK
  • 2008 - 2012, Master of Physics, University of Oxford, UK



Matti Zbinden
PhD Student

Mithun JR Edathil
Master Student


Controlled motility in the cyanobacterium Trichodesmium

Keywords: Trichodesmium, aggregation, gliding motility

The ocean’s nitrogen is largely fixed by cyanobacteria, including Trichodesmium, which forms aggregates comprising hundreds of filaments arranged in organized architectures. Aggregates often form upon exposure to stress and have ecological and biophysical characteristics that differ from those of single filaments. We found that Trichodesmium aggregates can rapidly modulate their shape, responding within minutes to changes in environmental conditions. Combining video microscopy and mathematical modeling, we discovered that this reorganization is mediated by “smart reversals” wherein gliding filaments reverse when their overlap with other filaments diminishes. By regulating smart reversals, filaments control aggregate architecture without central coordination. We propose that the modulation of gliding motility at the single-filament level is a determinant of Trichodesmium’s aggregation behavior and ultimately of its biogeochemical role in the ocean.

Marine snow formation by elongated phytoplankton

Keywords: biological pump, marine snow, encounter rates between sinking rods, collision kernels, turbulence

Marine microorganisms control the global biogeochemistry of the oceans through interactions between individual cells, as prominently exemplified by marine snow formation by elongated phytoplankton following a phytoplankton bloom. Current models of marine snow formation represent cells as spheres, yet phytoplankton cells are often highly elongated with typical aspect ratios of five and greater. To study the effect of elongation on marine snow formation, we recently derived the collision kernels between identical and dissimilar rods settling in a quiescent fluid and showed that marine snow formation by elongated phytoplankton can proceed efficiently even under quiescent conditions and that the resulting coagulation dynamics can lead to periodic bursts in the concentration of marine snow particles. More recently, in collaboration with Wilczek group, we included the effects of turbulent mixing on encounters and found that encounter rates between the most elongated cells are up to 10-fold higher than between spherical cells. We predict that these enhanced encounter rates accelerate marine snow formation and thus offer a mechanistic explanation for the rapid clearance of blooms.

Encounter rates between bacteria and sinking particles

Keywords: microbial ecology, marine snow, encounter rates, hydrodynamic focusing and screening, microswimmers in flow

The ecological interaction between bacteria and sinking particles, such as bacterial degradation of marine snow particles, is regulated by their encounters. We analytically and numerically quantified the encounter rate between sinking particles and non-motile or motile micro-organisms in the ballistic regime, explicitly accounting for the hydrodynamic shear created by the particle and its coupling with micro-organism shape. We complemented results with selected experiments on non-motile diatoms. Our results indicate that shear, which leads to hydrodynamic focusing and screening in the bacterium-particle system, should be taken into account to predict the interactions between bacteria and sinking particles responsible for the large carbon flux in the ocean's biological pump.

Spontaneous mirror symmetry breaking in 3D active fluids

Keywords: active fluids, active turbulence, helicity, inverse energy cascade, triadic interactions

Turbulence provides an important mechanism for energy redistribution and mixing in interstellar gases, planetary atmospheres, and the oceans. Classical turbulence theory suggests for ordinary 3D fluids or gases, such as water or air, that larger vortices can transform into smaller ones but not vice versa, thus limiting energy transfer from smaller to larger scales. Our calculations predict that bacterial suspensions and other pattern-forming active fluids can deviate from this paradigm by creating turbulent flow structures that spontaneously break mirror symmetry. These results imply that the collective dynamics of swimming microorganisms can enhance fluid mixing more strongly than previously thought.

Anomalous chained turbulence in actively driven flows on spheres

Keywords: active fluids, active turbulence, anomalous upward energy transfer in 2D turbulence

Recent experiments demonstrate the importance of substrate curvature for actively forced fluid dynamics. Yet, the covariant formulation and analysis of continuum models for nonequilibrium flows on curved surfaces still poses theoretical challenges. Here, we introduced and studied a generalized covariant Navier-Stokes model for fluid flows driven by active stresses in nonplanar geometries. The analytical tractability of the theory was demonstrated through exact stationary solutions for the case of a spherical bubble geometry. Direct numerical simulations revealed a curvature-induced transition from a burst phase to an anomalous turbulent phase that differs distinctly from externally forced classical 2D Kolmogorov turbulence. The coherent motion of the vortex chain network provides an efficient mechanism for upward energy transfer from smaller to larger scales, presenting an alternative to the conventional energy cascade in classical 2D turbulence.

Reduction of viscosity and inertia in active fluids

Keywords: active fluids, active fluid-structure interactions, viscosity reduction, Stokes' second problem

We investigated flow pattern formation and viscosity reduction mechanisms in active fluids by studying a generalized Navier-Stokes model that captures the experimentally observed bulk vortex dynamics in microbial suspensions. We presented exact analytical solutions including stress-free vortex lattices and introduced a computational framework that allows the efficient treatment of higher-order shear boundary conditions. Large-scale parameter scans identified the conditions for spontaneous flow symmetry breaking, geometry-dependent viscosity reduction, negative-viscosity states amenable to energy harvesting in confined suspensions and reduction of inertia in active fluids coupled to external pendulum. The theory uses only generic assumptions about the symmetries and long-wavelength structure of active stress tensors, suggesting that inviscid phases and reduction of inertia may be achievable in a broad class of nonequilibrium fluids by tuning confinement geometry and pattern scale selection.