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Optogenetic Control of Bacterial Cell-Cell Adhesion Dynamics: Unraveling the Influence on Biofilm Architecture and Functionality

Quispe Haro, Juan José (author), Chen, Fei (author), Los, R. (author), Shi, Shuqi (author), Sun, Wenjun (author), Chen, Yong (author), Idema, T. (author), Wegner, Seraphine V. (author)

The transition of bacteria from an individualistic to a biofilm lifestyle profoundly alters their biology. During biofilm development, the bacterial cell-cell adhesions are a major determinant of initial microcolonies, which serve as kernels for the subsequent microscopic and mesoscopic structure of the biofilm, and determine the resulting...

journal article 2024

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Circular Design Research in The Netherlands

den Hollander, M.C. (author), Idema, M.K. (author), Joore, Peter (author)

In 2023, the Netherlands is strategic partner of the Business of Design Week held in Hong Kong, with Circular Design as the central theme. One of the objectives of this partnership is to foster enduring international cooperation. As an initial step towards future collaborative efforts, the Network Applied Design Research (NADR) made an inventory...

book 2023

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The role of epidemic spreading in seizure dynamics and epilepsy surgery

Millán, Ana P. (author), van Straaten, Elisabeth C. W. (author), Stam, Cornelis J. (author), Nissen, Ida A. (author), Idema, Sander (author), Baayen, Johannes C. (author), Van Mieghem, P.F.A. (author), Hillebrand, Arjan (author)

Epilepsy surgery is the treatment of choice for drug-resistant epilepsy patients, but only leads to seizure freedom for roughly two in three patients. To address this problem, we designed a patient-specific epilepsy surgery model combining large-scale magnetoencephalography (MEG) brain networks with an epidemic spreading model. This simple...

journal article 2023

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Branched actin cortices reconstituted in vesicles sense membrane curvature

Baldauf, L. (author), Frey, F.F.F. (author), Arribas Perez, M. (author), Idema, T. (author), Koenderink, G.H. (author)

The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks...

journal article 2023

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Epidemic models characterize seizure propagation and the effects of epilepsy surgery in individualized brain networks based on MEG and invasive EEG recordings

Millán, Ana P. (author), van Straaten, Elisabeth C.W. (author), Stam, Cornelis J. (author), Nissen, Ida A. (author), Idema, Sander (author), Baayen, Johannes C. (author), Van Mieghem, P.F.A. (author), Hillebrand, Arjan (author)

Epilepsy surgery is the treatment of choice for drug-resistant epilepsy patients. However, seizure-freedom is currently achieved in only 2/3 of the patients after surgery. In this study we have developed an individualized computational model based on MEG brain networks to explore seizure propagation and the efficacy of different virtual...

journal article 2022

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Membrane area gain and loss during cytokinesis

Frey, F.F.F. (author), Idema, T. (author)

In cytokinesis of animal cells, the cell is symmetrically divided into two. Since the cell's volume is conserved, the projected area has to increase to allow for the change of shape. Here we aim to predict how membrane gain and loss adapt during cytokinesis. We work with a kinetic model in which membrane turnover depends on membrane tension...

journal article 2022

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A gastruloid model of the interaction between embryonic and extra-embryonic cell types

Berenger-Currias, N.M.L.P. (author), Mircea, Maria (author), Adegeest, Esmée (author), van den Berg, Patrick R. (author), Feliksik, Marleen (author), Hochane, Mazène (author), Idema, T. (author), Tans, S.J. (author), Semrau, Stefan (author)

Stem-cell derived in vitro systems, such as organoids or embryoids, hold great potential for modeling in vivo development. Full control over their initial composition, scalability, and easily measurable dynamics make those systems useful for studying specific developmental processes in isolation. Here we report the formation of gastruloids...

journal article 2022

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More than just a barrier: using physical models to couple membrane shape to cell function

Frey, F.F.F. (author), Idema, T. (author)

The correct execution of many cellular processes, such as division and motility, requires the cell to adopt a specific shape. Physically, these shapes are determined by the interplay of the plasma membrane and internal cellular driving factors. While the plasma membrane defines the boundary of the cell, processes inside the cell can result in...

review 2021

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Optimization of epilepsy surgery through virtual resections on individual structural brain networks

Nissen, Ida A. (author), Millán, Ana P. (author), Stam, Cornelis J. (author), van Straaten, Elisabeth C.W. (author), Douw, Linda (author), Pouwels, Petra J.W. (author), Idema, Sander (author), Baayen, Johannes C. (author), Velis, Demetrios (author), Van Mieghem, P.F.A. (author), Hillebrand, Arjan (author)

The success of epilepsy surgery in patients with refractory epilepsy depends upon correct identification of the epileptogenic zone (EZ) and an optimal choice of the resection area. In this study we developed individualized computational models based upon structural brain networks to explore the impact of different virtual resections on the...

journal article 2021

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Mechanics in biology

Idema, T. (author)

Mechanics plays a key role in life, from simple tasks like providing protective shielding to highly complex ones such as cell division. To understand mechanical properties on the organism level, we need to zoom in to its constituent cells, then zoom back out to see how they collectively build tissues.

journal article 2020

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Interactions between model inclusions on closed lipid bilayer membranes

Idema, T. (author), Kraft, Daniela J. (author)

Protein inclusions in the membranes of living cells interact via the deformations they impose on that membrane. Such membrane-mediated interactions lead to sorting and self-assembly of the inclusions, as well as to membrane remodelling, crucial for many biological processes. For the past decades, theory, numerical calculations and experiments...

review 2019

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Mechanics and Relativity

Idema, T. (author)

In Mechanics and Relativity, the reader is taken on a tour through time and space. Starting from the basic axioms formulated by Newton and Einstein, the theory of motion at both the everyday and the highly relativistic level is developed without the need of prior knowledge. The relevant mathematics is provided in an appendix. The text contains...

book 2018

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Printing of Patterned, Engineered E. coli Biofilms with a Low-Cost 3D Printer

Schmieden, D.T. (author), Basalo Vázquez, Samantha J. (author), Sangüesa, Héctor (author), van der Does, M. (author), Idema, T. (author), Meyer, A.S. (author)

Biofilms can grow on virtually any surface available, with impacts ranging from endangering the lives of patients to degrading unwanted water contaminants. Biofilm research is challenging due to the high degree of biofilm heterogeneity. A method for the production of standardized, reproducible, and patterned biofilm-inspired materials could...

journal article 2018

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Mechanical force induces mitochondrial fission

Helle, Sebastian Carsten Johannes (author), Feng, Q. (author), Aebersold, Mathias J. (author), Hirt, Luca (author), Grüter, Raphael R. (author), Vahid Belarghou, A. (author), Sirianni, Andrea (author), Mostowy, Serge (author), Snedeker, Jess G. (author), Šarić, Anđela (author), Idema, T. (author), Zambelli, Tomaso (author), Kornmann, Benoît (author)

Eukaryotic cells are densely packed with macromolecular complexes and intertwining organelles, continually transported and reshaped. Intriguingly, organelles avoid clashing and entangling with each other in such limited space. Mitochondria form extensive networks constantly remodeled by fission and fusion. Here, we show that mitochondrial...

journal article 2017

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Curvature variation controls particle aggregation on fluid vesicles

Vahid Belarghou, A. (author), Saric, Andela (author), Idema, T. (author)

Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these...

journal article 2017

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Pointlike Inclusion Interactions in Tubular Membranes

Vahid Belarghou, A. (author), Idema, T. (author)

Membrane tubes and tubular networks are ubiquitous in living cells. Inclusions like proteins are vital for both the stability and the dynamics of such networks. These inclusions interact via the curvature deformations they impose on the membrane. We analytically study the resulting membrane mediated interactions in strongly curved tubular...

journal article 2016

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Lipid membrane-mediated attraction between curvature inducing objects

Van Der Wel, Casper (author), Vahid Belarghou, A. (author), ŠariĆ, Andela (author), Idema, T. (author), Heinrich, Doris (author), Kraft, Daniela J. (author)

The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself mediates protein self-organization in these processes through minimization of membrane curvature energy....

journal article 2016

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Collective dynamics of soft active particles

Van Drongelen, R. (author), Pal, A. (author), Goodrich, C.P. (author), Idema, T. (author)

We present a model of soft active particles that leads to a rich array of collective behavior found also in dense biological swarms of bacteria and other unicellular organisms. Our model uses only local interactions, such as Vicsek-type nearest-neighbor alignment, short-range repulsion, and a local boundary term. Changing the relative strength...

journal article 2015

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Mechanical signaling via nonlinear wavefront propagation in a mechanically excitable medium

Idema, T. (author), Liu, A.J. (author)

Models that invoke nonlinear wavefront propagation in a chemically excitable medium are rife in the biological literature. Indeed, the idea that wavefront propagation can serve as a signaling mechanism has often been invoked to explain synchronization of developmental processes. In this paper we suggest a kind of signaling based not on diffusion...

journal article 2014

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Newton-Krylov Methods in Power Flow and Contingency Analysis

Idema, R. (author)

A power system is a system that provides for the generation, transmission, and distribution of electrical energy. Power systems are considered to be the largest and most complex man-made systems. As electrical energy is vital to our society, power systems have to satisfy the highest security and reliability standards. At the same time,...

doctoral thesis 2012