% % This file was created by the TYPO3 extension % bib % --- Timezone: CET % Creation date: 2024-03-29 % Creation time: 10-26-53 % --- Number of references % 18 % @Article { WorlitzerJGBHEAB2022, title = {Biophysical aspects underlying the swarm to biofilm transition}, journal = {Science Advances}, year = {2022}, month = {6}, day = {15}, volume = {8}, number = {24}, tags = {8.4,8.43,ActFluid}, DOI = {DOI: 10.1126/sciadv.abn8152}, author = {Worlitzer, V. M. and Jose, A. and Grinberg, I. and B{\"a}r, M. and Heidenreich, S. and Eldar, A. and Ariel, G. and Be´er, A.} } @Article { ReinkenHBK2022, title = {Ising-like critical behavior of vortex lattices in an active fluid}, journal = {Physical Review Letters}, year = {2022}, month = {1}, day = {27}, volume = {128}, number = {4}, pages = {048004}, tags = {8.4,8.43,ActFluid}, DOI = {10.1103/PhysRevLett.128.048004}, author = {Reinken, H and Heidenreich, S and B{\"a}r, M and Klapp, S.H.L} } @Article { WorlitzerABSBH2021, title = {Turbulence-induced clustering in compressible active fluids}, journal = {Soft Matter}, year = {2021}, month = {11}, day = {11}, volume = {2021}, number = {17}, pages = {10447-10457}, tags = {8.4,8.43,ActFluid}, DOI = {https://doi.org/10.1039/D1SM01276B}, author = {Worlitzer, V M and Ariel, G and Be'er, A and Stark, H and B{\"a}r, M and Heidenreich, S} } @Article { PeledRHBAB2021, title = {Heterogeneous bacterial swarms with mixed lengths}, journal = {Physical Review E}, year = {2021}, month = {3}, day = {29}, volume = {103}, number = {3}, pages = {032413}, tags = {8.4,8.43,ActFluid}, DOI = {10.1103/PhysRevE.103.032413}, author = {Peled, S and Ryan, S D and Heidenreich, S and B{\"a}r, M and Ariel, G and Be'er, A} } @Article { WorlitzerABSB2021, title = {Motility-induced clustering and meso-scale turbulence in active polar fluids}, journal = {New Journal of Physics}, year = {2021}, month = {3}, day = {10}, volume = {23}, pages = {033012}, tags = {8.4,ActFluid}, DOI = {10.1088/1367-2630/abe72d}, author = {Worlitzer, V M and Ariel, G and Be'er, A and Stark, H and B{\"a}r, M and Heidenreich, S} } @Article { ReinkenNHSBKA2020, title = {Organizing bacterial vortex lattices by periodic obstacle arrays}, journal = {Commun Phys}, year = {2020}, month = {5}, day = {7}, volume = {3}, number = {76}, tags = {8.4,8.43,ActFluid}, DOI = {10.1038/s42005-020-0337-z}, author = {Reinken, H and Nishiguchi, D and Heidenreich, S and Sokolov, A and B{\"a}r, M and Klapp, S H L and Aranson, I S} } @Article { BeaerIGKHBA2020, title = {A phase diagram for bacterial swarming}, journal = {Commun Phys}, year = {2020}, month = {4}, day = {3}, volume = {3}, number = {66}, tags = {8.4,ActFluid}, DOI = {10.1038/s42005-020-0327-1}, author = {Be´er, A and Ilkanaiv, B and Gross, R and Kearns, D B and Heidenreich, S and B{\"a}r, M and Ariel, G} } @Article { BarGHP2020, title = {Self-Propelled Rods: Insights and Perspectives for Active Matter}, journal = {Annual Review of Condensed Matter Physics}, year = {2020}, month = {3}, day = {1}, volume = {11}, pages = {441--466}, tags = {8.4,,ActFluid}, DOI = {10.1146/annurev-conmatphys-031119-050611}, author = {B{\"a}r, M and Gro{\ss}mann, R and Heidenreich, S and Peruani, F} } @Article { HeidenreichDKB2016, title = {Hydrodynamic length-scale selection in microswimmer suspensions}, journal = {Physical Review E}, year = {2016}, month = {8}, day = {29}, volume = {94}, number = {2}, pages = {020601}, tags = {8.4,8.43,ActFluid}, DOI = {10.1103/PhysRevE.94.020601}, author = {Heidenreich, S and Dunkel, J and Klapp, H.L and B{\"a}r, M} } @Article { Alonso_PhysD_2015, title = {Oscillations and uniaxial mechanochemical waves in a model of an active poroelastic medium: Application to deformation patterns in protoplasmic droplets of Physarum polycephalum}, journal = {Physica D}, year = {2016}, month = {4}, day = {1}, volume = {318}, pages = {58-69}, tags = {8.41, Spatio-Diff, ActFluid}, DOI = {10.1016/j.physd.2015.09.017}, author = {Alonso, S and Strachauer, U and Radszuweit, M and B{\"a}r, M and Hauser, M.J.B} } @Article { SH, title = {Generalized Swift-Hohenberg models for dense active suspensions}, journal = {Eur. Phys. J. E}, year = {2016}, volume = {39}, number = {10}, pages = {97}, tags = {8.4,8.43,ActFluid}, DOI = {10.1140/epje/i2016-16097-2}, author = {Oza, AU and Heidenreich, S and Dunkel, J} } @Article { Radszuweit2014, title = {An active poroelastic model for mechanochemical patterns in protoplasmic droplets of Physarum polycephalum}, journal = {PloS one}, year = {2014}, volume = {9}, number = {6}, pages = {e99220}, abstract = {Motivated by recent experimental studies, we derive and analyze a two-dimensional model for the contraction patterns observed in protoplasmic droplets of Physarum polycephalum. The model couples a description of an active poroelastic two-phase medium with equations describing the spatiotemporal dynamics of the intracellular free calcium concentration. The poroelastic medium is assumed to consist of an active viscoelastic solid representing the cytoskeleton and a viscous fluid describing the cytosol. The equations for the poroelastic medium are obtained from continuum force balance and include the relevant mechanical fields and an incompressibility condition for the two-phase medium. The reaction-diffusion equations for the calcium dynamics in the protoplasm of Physarum are extended by advective transport due to the flow of the cytosol generated by mechanical stress. Moreover, we assume that the active tension in the solid cytoskeleton is regulated by the calcium concentration in the fluid phase at the same location, which introduces a mechanochemical coupling. A linear stability analysis of the homogeneous state without deformation and cytosolic flows exhibits an oscillatory Turing instability for a large enough mechanochemical coupling strength. Numerical simulations of the model equations reproduce a large variety of wave patterns, including traveling and standing waves, turbulent patterns, rotating spirals and antiphase oscillations in line with experimental observations of contraction patterns in the protoplasmic droplets.}, keywords = {,Biological,Biomechanical Phenomena,Calcium,Calcium: metabolism,Cytoplasm,Cytoplasm: physiology,Cytoskeleton,Cytoskeleton: physiology,Elasticity,Mechanical,Models,Physarum polycephalum,Physarum polycephalum: cytology,Physarum polycephalum: physiology,Stress,pattern formation}, tags = {8.41, ActMatter, ActFluid}, web_url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099220}, publisher = {Public Library of Science}, ISSN = {1932-6203}, DOI = {10.1371/journal.pone.0099220}, author = {Radszuweit, M and Engel, H and B{\"a}r, M} } @Article { Heidenreich2014, title = {Numerical simulations of a minimal model for the fluid dynamics of dense bacterial suspensions}, journal = {J.Phys.: Conf. Ser.}, year = {2014}, volume = {490}, number = {1}, pages = {012126}, keywords = {8.43,fluid dynamics}, tags = {8.43, ActFluid}, web_url = {http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012126}, publisher = {IOP Publishing}, language = {en}, ISSN = {1742-6596}, DOI = {10.1088/1742-6596/490/1/012126}, author = {Heidenreich, S and Klapp, S H L and B{\"a}r, M} } @Article { Heiden_PRL2013, title = {Fluid Dynamics of Bacterial Turbulence}, journal = {Phys. Rev. Lett.}, year = {2013}, volume = {110}, pages = {228102}, tags = {8.43, ActFluid}, DOI = {10.1103/PhysRevLett.110.228102}, author = {Dunkel, J and Heidenreich, S and Drescher, K and Wensink, H. H and B{\"a}r, M and Goldstein, R. E} } @Article { Radszuweit2013, title = {Intracellular mechanochemical waves in an active poroelastic model}, journal = {Phys. Rev. Lett.}, year = {2013}, volume = {110}, number = {13}, pages = {138102}, abstract = {Many processes in living cells are controlled by biochemical substances regulating active stresses. The cytoplasm is an active material with both viscoelastic and liquid properties. We incorporate the active stress into a two-phase model of the cytoplasm which accounts for the spatiotemporal dynamics of the cytoskeleton and the cytosol. The cytoskeleton is described as a solid matrix that together with the cytosol as an interstitial fluid constitutes a poroelastic material. We find different forms of mechanochemical waves including traveling, standing, and rotating waves by employing linear stability analysis and numerical simulations in one and two spatial dimensions.}, keywords = {Biological,Biomechanical Phenomena,Cell Physiological Phenomena,Cytoplasm,Cytoplasm: chemistry,Cytoskeleton,Cytoskeleton: chemistry,Elasticity,Extracellular Fluid,Extracellular Fluid: chemistry,Models,Viscosity}, tags = {8.41, ActMatt, ActFluid}, web_url = {http://www.ncbi.nlm.nih.gov/pubmed/23581377}, ISSN = {1079-7114}, DOI = {10.1103/PhysRevLett.110.138102}, author = {Radszuweit, M and Alonso, S. and Engel, H and B{\"a}r, M} } @Article { Dunkel2013, title = {Minimal continuum theories of structure formation in dense active fluids}, journal = {New J. Phys.}, year = {2013}, volume = {15}, number = {4}, pages = {045016}, tags = {8.43, ActFluid}, web_url = {http://iopscience.iop.org/article/10.1088/1367-2630/15/4/045016}, publisher = {IOP Publishing}, language = {en}, ISSN = {1367-2630}, DOI = {10.1088/1367-2630/15/4/045016}, author = {Dunkel, J and Heidenreich, S and B{\"a}r, M and Goldstein, R E} } @Article { Wensink2012, title = {Meso-scale turbulence in living fluids}, journal = {Proc. Natl. Acad. Sci. U.S.A.}, year = {2012}, volume = {109}, number = {36}, pages = {14308--13}, abstract = {Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior among the simplest forms of life and is important for fluid mixing and molecular transport on the microscale. The mathematical characterization of turbulence phenomena in active nonequilibrium fluids proves even more difficult than for conventional liquids or gases. It is not known which features of turbulent phases in living matter are universal or system-specific or which generalizations of the Navier-Stokes equations are able to describe them adequately. Here, we combine experiments, particle simulations, and continuum theory to identify the statistical properties of self-sustained meso-scale turbulence in active systems. To study how dimensionality and boundary conditions affect collective bacterial dynamics, we measured energy spectra and structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D geometries. Our experimental results for the bacterial flow statistics agree well with predictions from a minimal model for self-propelled rods, suggesting that at high concentrations the collective motion of the bacteria is dominated by short-range interactions. To provide a basis for future theoretical studies, we propose a minimal continuum model for incompressible bacterial flow. A detailed numerical analysis of the 2D case shows that this theory can reproduce many of the experimentally observed features of self-sustained active turbulence.}, keywords = {Bacillus subtilis,Bacillus subtilis: physiology,Biological,Biomechanical Phenomena,Computer Simulation,Culture Media,Culture Media: chemistry,Hydrodynamics,Models,Movement,Movement: physiology}, tags = {8.43, ActFluid}, web_url = {http://www.pnas.org/content/109/36/14308}, ISSN = {1091-6490}, DOI = {10.1073/pnas.1202032109}, author = {Wensink, H H and Dunkel, J and Heidenreich, S and Drescher, K and Goldstein, R E and L{\"o}wen, H and Yeomans, J M} } @Article { Radszuweit2011, title = {A model for oscillations and pattern formation in protoplasmic droplets of Physarum polycephalum}, journal = {Eur. Phys. J. - Special Topics}, year = {2010}, volume = {191}, number = {1}, pages = {159--172}, keywords = {8.41,pattern formation}, tags = {8.41, ActMatter, ActFluid}, web_url = {http://www.springerlink.com/index/10.1140/epjst/e2010-01348-2}, ISSN = {1951-6355}, DOI = {10.1140/epjst/e2010-01348-2}, author = {Radszuweit, M and Engel, H and B{\"a}r, M} }