Category Archives: Physics

Scientific Article: A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems

I co-authored a scientific article in Journal of Computational Science.

A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction–advection–diffusion systems
Ingo Tischler, Florian Weik, Robert Kaufmann, Michael Kuron, Rudolf Weeber, Christian Holm
J. Comp. Sci. 63, 101770 (2022)
DOI: 10.1016/j.jocs.2022.101770

The journal does not provide open access to the article, but you can download it for free from chemRxiv: 10.26434/chemrxiv-2021-39nhv-v3.

Dissertation: Lattice Boltzmann methods for microswimmers in complex environments

My dissertation has been published by the university:

Lattice Boltzmann methods for microswimmers in complex environments
Michael Kuron
PhD thesis, Universität Stuttgart
DOI: 10.18419/opus-11926

Printed copies are available at the university library and at the national library in Frankfurt and Leipzig. I also have a few spare ones, so if you think you really need one, let me know. The SHA1 hash of the PDF file I submitted to the library is 45f8b26dc10c04a5221d79fa3a2c42478a2b89b6, which matches the file available online as of today.

Abstract

This dissertation introduces, validates, and applies various models for the study of microswimmers, predominantly focusing on the development of lattice algorithms. The models are applicable to biological swimmers like bacteria, but also to artificial ones propelled via chemical reactions. The unifying theme is a complex fluidic environment, ranging from Newtonian single-component fluids, to electrolyte solutions, to viscoelastic media flowing through arbitrary geometries. A particular focus is placed on resolving each swimmer’s surface since the propulsion, or phoresis, originates from a small layer of fluid around it. Resolving the propulsion mechanism is necessary to accurately study hydrodynamic interactions with obstacles and other swimmers. It is also a prerequisite for the study of taxis, that is, alignment with an external field such as a nutrient gradient. Similarly, phoretic interactions can be investigated, like when a swimmer senses and avoids the trail where another swimmer has already depleted the fuel.

Update January 2024

Here is an updated PDF with all the preprint citations replaced with the published versions. This should make it easier to find all references via the DOI system.

Scientific Article: An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids

I’ve published a scientific article in the European Physical Journal E.

An extensible lattice Boltzmann method for viscoelastic flows: complex and moving boundaries in Oldroyd-B fluids
Michael Kuron, Cameron Stewart, Joost de Graaf, and Christian Holm
European Physical Journal E 44, 1 (2021)
DOI:
10.1140/epje/s10189-020-00005-6

The article is available as open-access from the publisher, thanks to Projekt DEAL. One of my pictures even made it onto the cover of the January 2021 issue:

Scientific Article: waLBerla: A block-structured high-performance framework for multiphysics simulations

I co-authored a scientific article in Computesr & Mathematics with Applications:

waLBerla: A block-structured high-performance framework for multiphysics simulations
Martin Bauer, Sebastian Eibl, Christian Godenschwager, Nils Kohl, Michael Kuron, Christoph Rettinger, Florian Schornbaum, Christoph Schwarzmeier, Dominik Thönnes, Harald Köstler, and Ulrich Rüde
Comp. Math. Appl. 81, 478 (2021)
DOI:
10.1016/j.camwa.2020.01.007

The journal does not provide open access to the article, but you can download it for free from arXiv: arXiv:1909.13772.

What to do when Mathematica’s ParallelMap/ParallelTable takes a long time to start up

I have a Mathematica notebook that derives some rather massive expressions. I wanted to do some transformations on them in parallel using ParallelMap or ParallelTable, but noticed that these commands were only running on a single CPU core for hours before actually starting to run in parallel and occupy all CPU cores. While it was running on only that single CPU core, I could not even abort the evaluation using Alt-. like one usually can: it simply seemed stuck.

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;
a2 = make_massive_expression[a1];
a3 = make_massive_expression[a2];
as = {a1,a2,a3};

b = ParallelTable[process[as[[i]]], {i,Length[as]}];

As it turns out, during the startup phase Mathematica copies all definitions from the main kernel to the parallel kernels. And that seems to be a rather inefficient procedure. So let’s transfer the needed definitions manually.

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;
a2 = make_massive_expression[a1];
a3 = make_massive_expression[a2];
as = {a1,a2,a3};

DistributeDefinitions[as, process];
b = ParallelTable[process[as[[i]]], {i,Length[as]}, DistributedContexts -> None];

Now DistributeDefinitions is slow, but ParallelTable immediately starts running in parallel on multiple kernels. We haven’t gained anything by splitting things like this, but at least we can now tell exactly where the problem lies. So instead of transferring the massive expressions to the parallel kernels, let’s only transfer the simple expression and have the parallel kernels derive the massive expression themselves:

make_massive_expression[x_] := ...;
process[x_] := Simplify[x];
a1 = simple_expression;

DistributeDefinitions[a1, make_massive_expression, process];

ParallelEvaluate[(
   a2 = make_massive_expression[a1];
   a3 = make_massive_expression[a2];
   as = {a1,a2,a3}
), DistributedContexts -> None];

b = ParallelTable[process[as[[i]]], {i,Length[as]}, DistributedContexts -> None];

Scientific Article: Hydrodynamic mobility reversal of squirmers near flat and curved surfaces

I’ve published a scientific article in Soft Matter.

Hydrodynamic mobility reversal of squirmers near flat and curved surfaces
Michael Kuron, Philipp Stärk, Christian Holm, and Joost de Graaf
Soft Matter 15, 5908 (2019)
DOI:
10.1039/C9SM00692C

The journal does not provide open access to the article, but you can download it for free from arXiv: arXiv:1903.04799.

Scientific Article: A lattice Boltzmann model for squirmers

I’ve published a scientific article in The Journal of Chemical Physics.

A lattice Boltzmann model for squirmers
Michael Kuron, Philipp Stärk, Christian Burkard, Joost de Graaf, and Christian Holm
J. Chem Phys. 150, 144110 (2019)
DOI: 10.1063/1.5085765

The journal does not provide open access to the article, but you can download it for free from arXiv: arXiv:1903.04799.

Scientific Article: ESPResSo 4.0 — an extensible software package for simulating soft matter systems

I co-authored a scientific article in The European Physical Journal Special Topics:

ESPResSo 4.0 – an extensible software package for simulating soft matter systems
Florian Weik, Rudolf Weeber, Kai Szuttor, Konrad Breitsprecher, Joost de Graaf, Michael Kuron, Jonas Landsgesell, Henri Menke, David Sean, and Christian Holm
Eur. Phys. J. Spec. Top. 227, 1789 (2019)
DOI:
10.1140/epjst/e2019-800186-9

The journal does not provide open access to the article, but you can download it for free from arXiv: arXiv:1811.07729.

Scientific Article: Toward Understanding of Self-Electrophoretic Propulsion under Realistic Conditions: From Bulk Reactions to Confinement Effects

My colleague Patrick and I published a review article in Accounts of Chemical Research:

Scientific Article: Toward Understanding of Self-Electrophoretic Propulsion under Realistic Conditions: From Bulk Reactions to Confinement Effects
Michael Kuron, Patrick Kreissl, and Christian Holm
Accounts of Chemical Research 51, 2998 (2018)
DOI:
10.1021/acs.accounts.8b00285

Unfortunately there is no open-access version of this article.

Scientific Article: Moving charged particles in lattice Boltzmann-based electrokinetics

I’ve published a scientific article in The Journal of Chemical Physics.

Moving charged particles in lattice Boltzmann-based electrokinetics
Michael Kuron, Georg Rempfer, Florian Schornbaum, Martin Bauer, Christian Godenschwager, Christian Holm, and Joost de Graaf
J. Chem. Phys. 145, 214102 (2016)
DOI:10.1063/1.4968596

The journal provides open-access to the article for the first month. After that, you’ll still be able to download it for free from arXiv: arXiv:1607.04572.