Publications

Preprints

• G. Dadunashvili and T. Idema
  flippy: User friendly and open source framework for lipid membrane simulations
  arXiv/2301.12305.


• L. Baldauf, F. Frey, M. A. Perez, M. Mladenov, M. Way, T. Idema, G. H. Koenderink
  Biomimetic actin cortices shape cell-sized lipid vesicles
  bioRxiv/2023.01.15.524117.
  


• C. T. van de Kamp, G. Dadunashvili, J. L. A. Dubbeldam, T. Idema
  Emergent order in a continuous state adaptive network model of living systems
  arXiv/2103.04312.
  


• R. Los, D. van Holthe tot Echten, G. Nordemann, M. Wehrens, S. J. Tans, T. Idema
  Defect dynamics in growing bacterial colonies
  arXiv/2003.10509.
  


• A. Vahid, G. Dadunashvili and T. Idema
  Membrane-mediated interactions induce spontaneous filament bundling
  bioRxiv/2018/336545.
  

Published papers

• J. J. Quispe Haro, F. Chen, R. Los, S. Shi, W. Sun, Y. Chen, T. Idema, S. V. Wegner
  Optogenetic control of bacterial cell-cell adhesion dynamics: Unraveling the influence on biofilm architecture and functionality
  Advanced Science, 2310079 (2024) / doi 10.1002/advs.202310079.
  


• L. Baldauf, F. Frey, M. A. Perez, T. Idema, G. H. Koenderink
  Reconstituted branched actin networks sense and generate micron-scale membrane curvature
  Biophysical Journal 122, 2311-2324 (2023) / doi 10.1016/j.bpj.2023.02.018 / bioRxiv/2022.08.31.505969.
  


• F. Frey and T. Idema
  Membrane area gain and loss during cytokinesis
  Physical Review E 106, 024401 (2022) / doi 10.1103/PhysRevE.106.024401.
  


• N. M. L. P. Bérenger-Currias, M. Mircea, E. Adegeest, P. R. van den Berg, M. Feliksik, M. Hochane, T. Idema, S. J. Tans, S. Semrau
  A gastruloid model of the interaction between embryonic and extra-embryonic cell types
  Journal of Tissue Engineering 13, 20417314221103042 (2022) / doi 10.1177/20417314221103042 / bioRxiv/2020/947655.
  


• W. K. Spoelstra, J. M. Jacques, R. Gonzalez-Linares, F. L. Nóbrega, A. C. Haagsma, M. Dogterom, D. H. Meijer, T. Idema, S. J.J. Brouns, L. Reese
  CRISPR-based DNA and RNA detection with liquid phase separation
  Biophysical Journal 120, 1198-1209 (2021) / doi 10.1016/j.bpj.2021.02.013 / bioRxiv/2018/471482.
  


• F. Frey and T. Idema
  More than just a barrier: using physical models to couple membrane shape to cell function
  Soft Matter 17, 3533-3549 (2021) / doi 10.1039/D0SM01758B


• T. Idema
  Mechanics in biology
  Europhysics News 51/5, 28-30 (2020) / doi 10.1051/epn/2020504.
  


• D. R. McCusker, R. van Drongelen and T. Idema
  Active particle dynamics beyond the jamming density
  EPL 125, 36001 (2019) / doi 10.1209/0295-5075/125/36001 / arXiv:1611.09125.
  


• T. Idema and D. J. Kraft
  Interactions between model inclusions on closed lipid bilayer membranes
  Current Opinion in Colloid & Interface Science 40, 58-69 (2019), doi 10.1016/j.cocis.2019.01.006.
  


• R. van Drongelen, T. Vazquez-Faci, T. A. P. M. Huijben, M. van der Zee, and T. Idema
  Mechanics of epithelial tissue formation
  J. Theor. Biol. 454, 182-189 (2018) / doi 10.1016/j.jtbi.2018.06.002 / arXiv:1705.06205.
  


• D. T. Schmieden, S. J. Basalo Vázquez, H. Sangüesa, M. van der Does, T. Idema, and A. S. Meyer
  Printing of patterned, engineered E. coli biofilms with a low-cost 3D printer
  ACS Synthetic Biology 7(5), 1328–1337 (2018).
  


• S. C. J. Helle, Q. Feng, M. J. Aebersold, L. Hirt, R. R. Grüter, A. Vahid, A. Sirianni, S. Mostowy, J. G. Snedeker, A. Šarić, T. Idema, T. Zambelli, and B. Kornmann
  Mechanical force induces mitochondrial fission
  eLife 6: e30292 (2017).
  


• A. Vahid, A. Šarić, and T. Idema
  Curvature variation controls particle aggregation on fluid vesicles
  Soft Matter 13, 4924-4930 / arXiv:1703.00776 (2017).
  


• A. Vahid and T. Idema
  Point-like inclusion interactions in tubular membranes
  Phys. Rev. Lett. 117, 138102 / arXiv:1510.03610 (2016).
  


• C. van der Wel, A. Vahid, A. Šarić, T. Idema, D. Heinrich, and D. J. Kraft
  Lipid membrane-mediated attractions between curvature inducing objects
  Scientific Reports 6, 32825 / arXiv:1603.04644 (2016).
  


• R. van Drongelen and T. Idema
  Collective dynamics and motility of soft elliptical particles
  In: Knoop, V. L. and Daamen, W. (Eds.) Traffic and Granular Flow '15, 605-612, Springer, 2016.
  


• R. van Drongelen, A. Pal, C. P. Goodrich, and T. Idema
  Collective dynamics of soft active particles
  Phys. Rev. E 91, 032706 / arXiv:1411.4821 (2015).
  


• T. Idema and A. J. Liu
  Mechanical signaling via nonlinear wavefront propagation in a mechanically excitable medium
  Phys. Rev. E 89, 062709 / arXiv:1304.3657 (2014).
  


• S. Majkut, T. Idema, J. Swift, C. Krieger, A. J. Liu, and D. E. Discher
  Heart-specific stiffening in early embryos parallels matrix and myosin expression to optimize beating
  Current Biology 23, 2434-2439 (2013).
  


• T. Idema, J. O. Dubuis, L. Kang, M. L. Manning, P. C. Nelson, T. C. Lubensky, and A. J. Liu
  The syncytial Drosophila embryo as a mechanically excitable medium
  PLoS ONE 8, e77216 / arXiv:1304.4025 (2013).
  Drosophila embryo development movie.
  


• T. Idema
  A new way of tracking motion, shape and divisions
  Eur. Biophys. J. 42, 647-654 (2013).
  


• T. Idema and C. Storm
  Analytical expressions for the shape of axisymmetric membranes with multiple domains
  Eur. Phys. J. E 34, 67 (2011).
  


• P. M. Shaklee, T. Idema, L. Bourel-Bonnet, M. Dogterom, and T. Schmidt
  Kinesin recycling in stationary membrane tubes
  Biophys. J. 99, 1835-1841 (2010).
  


• T. Idema, S. Semrau, C. Storm, and T. Schmidt
  Membrane mediated sorting
  Phys. Rev. Lett. 104, 198102 (2010).
  


• T. Idema
  Structuur, vorm en dynamica van biologische membranen
  Nederlands Tijdschrift voor Natuurkunde, 76-04, 99-101 (2010).
  


• M. Basan, T. Idema, M. Lenz, J.-F. Joanny, and T. Risler
  A reaction-diffusion model of the cadherin-catenin system: A possible mechanism for contact inhibition and implications for tumorigenesis
  Biophys. J. 98, 2770-2779 / arXiv:1505.00764 (2010).
  


• T. Idema, J.M.J. van Leeuwen, and C. Storm
  Phase coexistence and line tension in ternary lipid systems
  Phys. Rev. E 80, 041924 (2009).
  


• S. Semrau, T. Idema, T. Schmidt, and C. Storm
  Membrane mediated interactions measured using membrane domains
  Biophys. J. 96, 4906-4915 (2009).
  


• P. M. Shaklee, T. Idema, G. Koster, C. Storm, T. Schmidt, and M. Dogterom
  Bidirectional membrane tube dynamics driven by nonprocessive motors
  Proc. Natl. Acad. Sci. USA 105, 7993-7997 (2008).
  


• S. Semrau, T. Idema, L. Holtzer, T. Schmidt, and C. Storm
  Accurate determination of elastic parameters for multi-component membranes
  Phys. Rev. Lett. 100, 088101 / arXiv:cond-mat/0612554 (2008).
  

Books

T. Idema Introduction to particle and continuum mechanics November 2023 doi 10.59490/tb.81
T. Idema Mechanics and Relativity October 2018 ISBN 978-94-6366-087-7 (hardcopy) / 978-94-6366-085-3 (ebook)

Book chapters

• T. Idema
  Membranes and vesicles
  In: Lecture notes of the 49^th IFF spring school `Physics of Life', G. Gompper et al. (Eds.), section C1 (2018).
  

Software

• G. Dadunashvili
  Flippy - a C++20 package for dynamically triangulated membrane simulations
  Project page on github.
  Documentation.

PhD theses

G. Dadunashvili Physical principles of membrane reshaping September 21, 2022 ISBN 978-90-8593-535-3 doi 10.4233/uuid:4971c301-0234-4762-8a67-74337f6acbbc
N.M.L.P. Bérenger-Currias Embryonic stem cell-based in vitro models to study early mammalian development February 23, 2022 ISBN 978-90-8593-514-8 doi 10.4233/uuid:83a1b783-67b5-4b93-8d6a-705f4d8edf65 Noémie did most of her research work in the Semrau lab in Leiden, and was also co-supervised by Sander Tans.
A. Vahid Assembly of membrane-deforming objects in tubular and vesicular membranes October 17, 2018 ISBN 978-90-8593-365-6 doi 10.4233/uuid:e6df2051-7db1-4316-9867-c800be313c13 Afshin got his PhD cum laude and also won the TU Delft Kavli thesis prize.
R. van Drongelen Collective dynamics and jamming in biological systems July 2, 2018 ISBN 978-90-8593-354-0 doi 10.4233/uuid:2748fa8b-8728-4931-8de1-2307322ef40c
T. Idema Structure, shape and dynamics of biological membranes November 19, 2009 ISBN 978-90-8593-060-0