Matti Zbinden
PhD Student
Jonasz Słomka
LaTeX: Jonasz S\l{}omka
ETH Zürich
Institute of Environmental Engineering
LauraHeznerWeg 7, HIF D22.1
8093 Zürich
Switzerland
email: jslomka "at" ethz.ch
I am a junior group leader (SNF Ambizione Fellow) at the Institute of Environmental Engineering at ETH Zürich. Previously, I was a postdoctoral 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
Dates:
Group
Mithun JR Edathil
Master Student
Research
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 singlefilament level is a determinant of Trichodesmium’s aggregation behavior and ultimately of its biogeochemical role in the ocean.

Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture
U. Pfreundt*, J. Słomka*, G. Schneider, A. Sengupta, F. Carrara, V. Fernandez, M. Ackermann and R. Stocker
Science, 380: 830835, 2023
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 10fold 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.

Elongation enhances encounter rates between phytoplankton in turbulence
J.A. ArguedasLeiva*, J. Słomka*, C. C. Lalescu, R. Stocker and M. Wilczek
Proc. Natl. Acad. Sci. U.S.A., 119: e2203191119, 2022 
Bursts characterize coagulation of rods in a quiescent fluid
J. Słomka and R. Stocker
Phys. Rev. Lett. , 124: 258001, 2020 
On the collision of rods in a quiescent fluid
J. Słomka and R. Stocker
Proc. Natl. Acad. Sci. U.S.A. , 117: 33723374, 2020
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 nonmotile or motile microorganisms in the ballistic regime, explicitly accounting for the hydrodynamic shear created by the particle and its coupling with microorganism shape. We complemented results with selected experiments on nonmotile diatoms. Our results indicate that shear, which leads to hydrodynamic focusing and screening in the bacteriumparticle 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.

Encounter rates between bacteria and small sinking particles
J. Słomka, U. Alcolombri, E. Secchi, R. Stocker and V. I. Fernandez
New J. Phys. , 22: 043016, 2020
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 patternforming 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.

The nature of triad interactions in active turbulence
J. Słomka, P. Suwara and J. Dunkel
J. Fluid Mech. , 841: 701–731, 2018 
Spontaneous mirrorsymmetry breaking induces inverse energy cascade in 3D active fluids
J. Słomka and J. Dunkel
Proc. Natl. Acad. Sci. U.S.A. , 114: 21192124, 2017
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 NavierStokes 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 curvatureinduced 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.

Anomalous chained turbulence in actively driven flows on spheres
O. Mickelin*, J. Słomka*, K. J. Burns, D. Lecoanet, G. M. Vasil, L. M. Faria and J. Dunkel
Phys. Rev. Lett. , 120: 164503, 2018
Reduction of viscosity and inertia in active fluids
Keywords: active fluids, active fluidstructure interactions, viscosity reduction, Stokes' second problem
We investigated flow pattern formation and viscosity reduction mechanisms in active fluids by studying a generalized NavierStokes model that captures the experimentally observed bulk vortex dynamics in microbial suspensions. We presented exact analytical solutions including stressfree vortex lattices and introduced a computational framework that allows the efficient treatment of higherorder shear boundary conditions. Largescale parameter scans identified the conditions for spontaneous flow symmetry breaking, geometrydependent viscosity reduction, negativeviscosity 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 longwavelength 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.

Stokes’ second problem and reduction of inertia in active fluids
J. Słomka, A. Townsend and J. Dunkel
Phys. Rev. Fluids , 3: 103304, 2018 
Geometrydependent viscosity reduction in sheared active fluids
J. Słomka and J. Dunkel
Phys. Rev. Fluids , 2: 043102, 2017
Publications

Vortex line entanglement in active Beltrami flows
N. Romeo, J. Słomka, J. Dunkel and K. J. Burns
J. Fluid Mech., 982: A12, 2024 
Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture
U. Pfreundt*, J. Słomka*, G. Schneider, A. Sengupta, F. Carrara, V. Fernandez, M. Ackermann and R. Stocker
Science, 380: 830835, 2023 
Encounter rates prime interactions between microorganisms
J. Słomka, U. Alcolombri, F. Carrara, R. Foffi, F. J. Peaudecerf, M. Zbinden and R. Stocker
Interface Focus, 13: 20220059, 2023 
Elongation enhances encounter rates between phytoplankton in turbulence
J.A. ArguedasLeiva*, J. Słomka*, C. C. Lalescu, R. Stocker and M. Wilczek
Proc. Natl. Acad. Sci. U.S.A., 119: e2203191119, 2022 
A microfluidic platform for characterizing the structure and rheology of biofilm streamers
G. Savorana, J. Słomka, R. Stocker, R. Rusconi and E. Secchi
Soft Matter, 18: 38783890, 2022 
ARC: An Open WebPlatform for Request/Supply Matching for a Prioritized and Controlled COVID19 Response
J.D. Courcol, et al.
Front. Public Health, 9: 607677, 2021 
Bursts characterize coagulation of rods in a quiescent fluid
J. Słomka and R. Stocker
Phys. Rev. Lett., 124: 258001, 2020 
Encounter rates between bacteria and small sinking particles
J. Słomka, U. Alcolombri, E. Secchi, R. Stocker and V. I. Fernandez
New J. Phys., 22: 043016, 2020 
On the collision of rods in a quiescent fluid
J. Słomka and R. Stocker
Proc. Natl. Acad. Sci. U.S.A., 117: 33723374, 2020 
Stokes’ second problem and reduction of inertia in active fluids
J. Słomka, A. Townsend and J. Dunkel
Phys. Rev. Fluids, 3: 103304, 2018 
The nature of triad interactions in active turbulence
J. Słomka, P. Suwara and J. Dunkel
J. Fluid Mech., 841: 701–731, 2018 
Anomalous chained turbulence in actively driven flows on spheres
O. Mickelin*, J. Słomka*, K. J. Burns, D. Lecoanet, G. M. Vasil, L. M. Faria and J. Dunkel
Phys. Rev. Lett., 120: 164503, 2018 
Spontaneous mirrorsymmetry breaking induces inverse energy cascade in 3D active fluids
J. Słomka and J. Dunkel
Proc. Natl. Acad. Sci. U.S.A., 114: 21192124, 2017 
Geometrydependent viscosity reduction in sheared active fluids
J. Słomka and J. Dunkel
Phys. Rev. Fluids, 2: 043102, 2017 
Generalized NavierStokes equations for active suspensions
J. Słomka and J. Dunkel
Eur. Phys. J. Spec. Top., 224: 13491358, 2015