Publications

Articles:

Fluid flows shaping organism morphology.
Karen Alim,
Philos. Trans. Royal Soc. B in press (2018). (PDF)

Spatial mapping reveals multi-step pattern of wound healing in Physarum polycephalum.
Felix Bäuerle, Mirna Kramar & Karen Alim,
J. Phys. D: Appl. Phys., 50, 434005 (2017). (PDF)

Local pore size correlations determine flow distributions in porous media.
Karen Alim, Shima Parsa, David A. Weitz, & Michael P. Brenner,
Phys. Rev. Lett., 119, 144501 (2017). (PDF)

Quantifying enzyme activity in living cells.
Agnes Zotter, Felix Bäuerle, Debabrata Dey, Vladimir Kiss & Gideon Schreiber
J. Biol. Chem. 292: 15838 (2017).

Flow rate of transport network controls uniform metabolite supply to
tissue.

Felix J. Meigel & Karen Alim,
arXiv:1707.05616 (2017). (PDF)

Mechanism of signal propagation in Physarum polycephalum.
Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner,
Proc. Natl. Acad. Sci. U.S.A.,114(20), 5236-5141 (2017). (PDF) (Press German) (Press English)

Direct determination of enzyme kinetic parameters from single reactions using a new progress curve analysis tool.
Felix Bäuerle, Agnes Zotter & Gideon Schreiber
Protein Eng. Des. Sel. 30(3), 151–158 (2017).

Pruning to increase Taylor dispersion in Physarum polycephalum networks.
Sophie Marbach, Karen Alim, Natalie Andrew, Anne Pringle & Michael P. Brenner ,
Phys. Rev. Lett., 117, 178103 (2016). (PDF)

Leaf growth is conformal.
Karen Alim, Shahaf Armon, Boris I. Shraiman & Arezki Boudaoud ,
Phys. Biol., 13(5), 05LT01 (2016). (PDF)

Matrix elasticity of void-forming hydrogels controls transplanted-stem-cell-mediated bone formation.

Nathaniel Huebsch, Evi Lippens, Kangwon Lee, Manav Mehta, Sandeep T. Koshy, Max C. Darnell, Rajiv M. Desai, Christopher M. Madl, Maria Xu, Xuanhe Zhao, Ovijit Chaudhuri, Catia Verbeke, Woo Seob Kim, Karen Alim, Akiko Mammoto, Donald E. Ingber, Georg N. Duda & David J. Mooney ,
Nat. Mat., 14(12), 1269-1277 (2015). (PDF)

Quickguide: Physarum.
Karen Alim, Natalie Andrew and Anne Pringle,
Curr. Biol., 23(24), R1082-R1083 (2013). (PDF)

Being squeezed into the right place within the egg shell.
Karen Alim,
Biophys. J., 105(8), 1735-1736 (2013). (PDF)

Random network peristalsis in Physarum polycephalums organizes fluid flows across an individual.
Karen Alim*, Gabriel Amselem*, François Peaudecerf, Michael P. Brenner and Anne Pringle,
Proc. Natl. Acad. Sci. U.S.A., 110(33), 13306-13311 (2013). (PDF)

Regulatory role of cell division rules on tissue growth heterogeneity.
Karen Alim, Olivier Hamant and Arezki Boudaoud,
Front. Plant Sci. 3, 00174 (2012). (PDF)

Mechanical stress acts via katanin to amplify differences in growth rate between adjacent cells in Arabidopsis.
Magalie Uyttewaal*, Agata Burian*, Karen Alim*, Benoît Landrein, Dorota Borowska-Wykręt, Annick Dedieu, Alexis Peaucelle, Michał Ludynia, Jan Traas, Arezki Boudaoud**, Dorota Kwiatkowska** and Olivier Hamant**,
Cell 149, 439-451 (2012). (PDF)

Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides.
Severin Schink, Stephan Renner, Karen Alim, Vera Arnaut, Friedrich C. Simmel and Ulrich Gerland,
Biophys. J. 102, 85-95 (2012). (PDF)

Confinement induces conformational transition of semiflexible polymer rings to figure eight form.
Katja Ostermeir*, Karen Alim* and Erwin Frey,
Soft Matter 6, 3467-3471 (2010). arXiv:1004.4574. (PDF)

Quantitative predictions on auxin-induced polar distribution of PIN proteins during vein formation in leaves.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 33, 165 (2010). arXiv:1005.3768. (PDF)

Buckling of stiff polymer rings in weak spherical confinement.
Katja Ostermeir, Karen Alim and Erwin Frey,
Phys. Rev. E 81, 061802 (2010). arXiv:1003.4267. (PDF)

Excluded volume effects on semiflexible ring polymers.
Fabian Drube, Karen Alim, Guillaume Witz, Giovanni Dietler and Erwin Frey,
Nano Letters 10, 1445-1449 (2010). arXiv:0906.3991. (PDF)

Fluctuating semiflexible polymer ribbon constrained to a ring.
Karen Alim and Erwin Frey,
Eur. Phys. J. E 24, 185-191 (2007). arXiv:0708.0111. (PDF)

Shapes of semiflexible polymer rings.
Karen Alim and Erwin Frey,
Phys. Rev. Lett. 99, 198102 (2007). arXiv:q-bio/0703049. (PDF)

Drowsy cheetah hunting antelopes: A diffusing predator seeking fleeing prey.
Karen Winkler and Alan J. Bray,
J. Stat. Mech P02005 (2005). arXiv:cond-mat/0410449. (PDF)

Vicious walkers in a potential.
Alan J. Bray and Karen Winkler,
J. Phys. A 37, 5493 (2004). arXiv:cond-mat/0403220. (PDF)

Theses:

Shape and structure in biological systems.
PhD Thesis, Ludwig-Maximilians-Universität München (2010). (PDF)

Statistical mechanics of fluctuating polymer rings.

Diploma Thesis, Ludwig-Maximilians-Universität München (2006). (PDF)

Vicious walkers in one-body potentials.
Master Thesis, University of Manchester (2004). (PDF)