@article{AdamatzkySchnaussHuber2019, author = {Adamatzky, Andrew and Schnauß, J{\"o}rg and Huber, Florian}, title = {Actin droplet machine}, series = {Royal Society Open Science}, volume = {6}, journal = {Royal Society Open Science}, number = {12}, publisher = {Royal Soc. Publ.}, issn = {2054-5703}, doi = {10.1098/rsos.191135}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34675}, year = {2019}, abstract = {The actin droplet machine is a computer model of a three-dimensional network of actin bundles developed in a droplet of a physiological solution, which implements mappings of sets of binary strings. The actin bundle network is conductive to travelling excitations, i.e. impulses. The machine is interfaced with an arbitrary selected set of k electrodes through which stimuli, binary strings of length k represented by impulses generated on the electrodes, are applied and responses are recorded. The responses are recorded in a form of impulses and then converted to binary strings. The machine's state is a binary string of length k: if there is an impulse recorded on the ith electrode, there is a '1' in the ith position of the string, and '0' otherwise. We present a design of the machine and analyse its state transition graphs. We envisage that actin droplet machines could form an elementary processor of future massive parallel computers made from biopolymers.}, language = {en} } @article{AdamatzkyHuberSchnauss2019, author = {Adamatzky, Andrew and Huber, Florian and Schnauß, J{\"o}rg}, title = {Computing on actin bundles network}, series = {Scientific Reports}, volume = {9}, journal = {Scientific Reports}, number = {1}, publisher = {Springer Nature}, issn = {2045-2322}, doi = {10.1038/s41598-019-51354-y}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34665}, year = {2019}, abstract = {Actin filaments are conductive to ionic currents, mechanical and voltage solitons. These travelling localisations can be utilised to generate computing circuits from actin networks. The propagation of localisations on a single actin filament is experimentally unfeasible to control. Therefore, we consider excitation waves propagating on bundles of actin filaments. In computational experiments with a two-dimensional slice of an actin bundle network we show that by using an arbitrary arrangement of electrodes, it is possible to implement two-inputs-one-output circuits.}, language = {en} } @article{MiguelesRowlandsHuberetal.2019, author = {Migueles, Jairo H. and Rowlands, Alex V. and Huber, Florian and Sabia, S{\´e}verine and van Hees, Vincent T.}, title = {GGIR: A Research Community-Driven Open Source R Package for Generating Physical Activity and Sleep Outcomes From Multi-Day Raw Accelerometer Data}, series = {Journal for the Measurement of Physical Behaviour}, volume = {2}, journal = {Journal for the Measurement of Physical Behaviour}, number = {3}, publisher = {Human Kinetics}, issn = {2575-6605}, doi = {10.1123/jmpb.2018-0063}, pages = {188 -- 196}, year = {2019}, language = {en} } @article{BeniddirKangGentaJouveetal.2021, author = {Beniddir, Mehdi A. and Kang, Kyo Bin and Genta-Jouve, Gr{\´e}gory and Huber, Florian and Rogers, Simon and van der Hooft, Justin J. J.}, title = {Advances in decomposing complex metabolite mixtures using substructure- and network-based computational metabolomics approaches}, series = {Natural Product Reports}, volume = {38}, journal = {Natural Product Reports}, number = {11}, publisher = {The Royal Society of Chemistry}, issn = {1460-4752}, doi = {10.1039/D1NP00023C}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34772}, pages = {1967 -- 1993}, year = {2021}, language = {en} } @article{HuberStrehleSchnaussetal.2015, author = {Huber, Florian and Strehle, Dan and Schnauß, J{\"o}rg and K{\"a}s, Josef}, title = {Formation of regularly spaced networks as a general feature of actin bundle condensation by entropic forces}, series = {New Journal of Physics}, volume = {17}, journal = {New Journal of Physics}, number = {4}, publisher = {IOP Publishing}, issn = {1367-2630}, doi = {10.1088/1367-2630/17/4/043029}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34833}, year = {2015}, language = {en} } @article{HuberVerhoevenMeijeretal.2020, author = {Huber, Florian and Verhoeven, Stefan and Meijer, Christiaan and Spreeuw, Hanno and Castilla, Efra{\´i}n and Geng, Cunliang and van der Hooft, Justin J. J. and Rogers, Simon and Belloum, Adam and Diblen, Faruk and Spaaks, Jurriaan H.}, title = {matchms - processing and similarity evaluation of mass spectrometry data}, series = {Journal of Open Source Software}, volume = {5}, journal = {Journal of Open Source Software}, number = {52}, publisher = {Cold Spring Harbor Laboratory}, issn = {2475-9066}, doi = {10.21105/joss.02411}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34856}, pages = {2411}, year = {2020}, language = {en} } @article{HuberKaesStuhrmann2008, author = {Huber, Florian and K{\"a}s, Josef and Stuhrmann, Bj{\"o}rn}, title = {Growing actin networks form lamellipodium and lamellum by self-assembly}, series = {Biophysical Journal}, volume = {95}, journal = {Biophysical Journal}, number = {12}, publisher = {Biophysical Society}, issn = {1542-0086}, doi = {10.1529/biophysj.108.134817}, pages = {5508 -- 5523}, year = {2008}, abstract = {Many different cell types are able to migrate by formation of a thin actin-based cytoskeletal extension. Recently, it became evident that this extension consists of two distinct substructures, designated lamellipodium and lamellum, which differ significantly in their kinetic and kinematic properties as well as their biochemical composition. We developed a stochastic two-dimensional computer simulation that includes chemical reaction kinetics, G-actin diffusion, and filament transport to investigate the formation of growing actin networks in migrating cells. Model parameters were chosen based on experimental data or theoretical considerations. In this work, we demonstrate the system's ability to form two distinct networks by self-organization. We found a characteristic transition in mean filament length as well as a distinct maximum in depolymerization flux, both within the first 1-2 microm. The separation into two distinct substructures was found to be extremely robust with respect to initial conditions and variation of model parameters. We quantitatively investigated the complex interplay between ADF/cofilin and tropomyosin and propose a plausible mechanism that leads to spatial separation of, respectively, ADF/cofilin- or tropomyosin-dominated compartments. Tropomyosin was found to play an important role in stabilizing the lamellar actin network. Furthermore, the influence of filament severing and annealing on the network properties is explored, and simulation data are compared to existing experimental data.}, language = {en} } @article{HuberKaes2011, author = {Huber, Florian and K{\"a}s, Josef}, title = {Self-regulative organization of the cytoskeleton}, series = {Cytoskeleton}, volume = {68}, journal = {Cytoskeleton}, number = {5}, publisher = {Wiley}, issn = {1949-3592}, doi = {10.1002/cm.20509}, pages = {259 -- 265}, year = {2011}, abstract = {Despite its impressive complexity the cytoskeleton succeeds to persistently organize itself and thus the cells' interior. In contrast to classical man-made machines, much of the cellular organization originates from inherent self-assembly and self-organization allowing a high degree of autonomy for various functional units. Recent experimental and theoretical studies revealed numerous examples of cytoskeleton components that arrange and organize in a self-regulative way. In the present review we want to shortly summarize some of the principle mechanisms that are able to inherently trigger and regulate the cytoskeleton organization. Although taken individually most of these regulative principles are rather simple with intuitively predictable consequences, combinations of two or more of these mechanisms can quickly give rise to very complex, unexpected behavior and might even be able to explain the formation of different functional units out of a common pool of available building blocks.}, language = {en} } @article{StuhrmannHuberKaes2011, author = {Stuhrmann, Bj{\"o}rn and Huber, Florian and K{\"a}s, Josef}, title = {Robust organizational principles of protrusive biopolymer networks in migrating living cells}, series = {Plos One}, volume = {6}, journal = {Plos One}, number = {1}, publisher = {Public Library of Science (PLoS)}, issn = {1932-6203}, doi = {10.1371/journal.pone.0014471}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34901}, year = {2011}, abstract = {Cell migration is associated with the dynamic protrusion of a thin actin-based cytoskeletal extension at the cell front, which has been shown to consist of two different substructures, the leading lamellipodium and the subsequent lamellum. While the formation of the lamellipodium is increasingly well understood, organizational principles underlying the emergence of the lamellum are just beginning to be unraveled. We report here on a 1D mathematical model which describes the reaction-diffusion processes of a polarized actin network in steady state, and reproduces essential characteristics of the lamellipodium-lamellum system. We observe a steep gradient in filament lengths at the protruding edge, a local depolymerization maximum a few microns behind the edge, as well as a differential dominance of the network destabilizer ADF/cofilin and the stabilizer tropomyosin. We identify simple and robust organizational principles giving rise to the derived network characteristics, uncoupled from the specifics of any molecular implementation, and thus plausibly valid across cell types. An analysis of network length dependence on physico-chemical system parameters implies that to limit array treadmilling to cellular dimensions, network growth has to be truncated by mechanisms other than aging-induced depolymerization, e.g., by myosin-associated network dissociation at the transition to the cell body. Our work contributes to the analytical understanding of the cytoskeletal extension's bisection into lamellipodium and lamellum and sheds light on how cells organize their molecular machinery to achieve motility.}, language = {en} } @article{PreciadoLopezHuberGrigorievetal.2014, author = {Preciado L{\´o}pez, Magdalena and Huber, Florian and Grigoriev, Ilya and Steinmetz, Michel O. and Akhmanova, Anna and Koenderink, Gijsje H. and Dogterom, Marileen}, title = {Actin-microtubule coordination at growing microtubule ends}, series = {Nature Communications}, volume = {5}, journal = {Nature Communications}, publisher = {Springer Nature}, issn = {2041-1723}, doi = {10.1038/ncomms5778}, url = {http://nbn-resolving.de/urn:nbn:de:hbz:due62-opus-34878}, pages = {4778}, year = {2014}, abstract = {To power dynamic processes in cells, the actin and microtubule cytoskeletons organize into complex structures. Although it is known that cytoskeletal coordination is vital for cell function, the mechanisms by which cross-linking proteins coordinate actin and microtubule activities remain poorly understood. In particular, it is unknown how the distinct mechanical properties of different actin architectures modulate the outcome of actin-microtubule interactions. To address this question, we engineered the protein TipAct, which links growing microtubule ends via end-binding proteins to actin filaments. We show that growing microtubules can be captured and guided by stiff actin bundles, leading to global actin-microtubule alignment. Conversely, growing microtubule ends can transport, stretch and bundle individual actin filaments, thereby globally defining actin filament organization. Our results provide a physical basis to understand actin-microtubule cross-talk, and reveal that a simple cross-linker can enable a mechanical feedback between actin and microtubule organization that is relevant to diverse biological contexts.}, language = {en} }