This file was created by the TYPO3 extension bib --- Timezone: CEST Creation date: 2024-04-16 Creation time: 06-54-33 --- Number of references 18 article WorlitzerJGBHEAB2022 Science Advances 2022 6 15 8 24 8.4,8.43,ActFluid DOI: 10.1126/sciadv.abn8152 V. M.Worlitzer A.Jose I.Grinberg M.Bär S.Heidenreich A.Eldar G.Ariel A.Be´er article ReinkenHBK2022 Physical Review Letters 2022 1 27 128 4 048004 8.4,8.43,ActFluid 10.1103/PhysRevLett.128.048004 HReinken SHeidenreich MBär S.H.LKlapp article WorlitzerABSBH2021 Soft Matter 2021 11 11 2021 17 10447-10457 8.4,8.43,ActFluid https://doi.org/10.1039/D1SM01276B V MWorlitzer GAriel ABe'er HStark MBär SHeidenreich article PeledRHBAB2021 Physical Review E 2021 3 29 103 3 032413 8.4,8.43,ActFluid 10.1103/PhysRevE.103.032413 SPeled S DRyan SHeidenreich MBär GAriel ABe'er article WorlitzerABSB2021 New Journal of Physics 2021 3 10 23 033012 8.4,ActFluid 10.1088/1367-2630/abe72d V MWorlitzer GAriel ABe'er HStark MBär SHeidenreich article ReinkenNHSBKA2020 Commun Phys 2020 5 7 3 76 8.4,8.43,ActFluid 10.1038/s42005-020-0337-z HReinken DNishiguchi SHeidenreich ASokolov MBär S H LKlapp I SAranson article BeaerIGKHBA2020 Commun Phys 2020 4 3 3 66 8.4,ActFluid 10.1038/s42005-020-0327-1 ABe´er BIlkanaiv RGross D BKearns SHeidenreich MBär GAriel article BarGHP2020 Annual Review of Condensed Matter Physics 2020 3 1 11 441--466 8.4,,ActFluid 10.1146/annurev-conmatphys-031119-050611 MBär RGroßmann SHeidenreich FPeruani article HeidenreichDKB2016 Physical Review E 2016 8 29 94 2 020601 8.4,8.43,ActFluid 10.1103/PhysRevE.94.020601 SHeidenreich JDunkel H.LKlapp MBär article Alonso_PhysD_2015 Physica D 2016 4 1 318 58-69 8.41, Spatio-Diff, ActFluid 10.1016/j.physd.2015.09.017 SAlonso UStrachauer MRadszuweit MBär M.J.BHauser article SH Eur. Phys. J. E 2016 39 10 97 8.4,8.43,ActFluid 10.1140/epje/i2016-16097-2 AUOza SHeidenreich JDunkel article Radszuweit2014 PloS one 2014 9 6 e99220 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. ,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 8.41, ActMatter, ActFluid http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099220 Public Library of Science 1932-6203 10.1371/journal.pone.0099220 MRadszuweit HEngel MBär article Heidenreich2014 J.Phys.: Conf. Ser. 2014 490 1 012126 8.43,fluid dynamics 8.43, ActFluid http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012126 IOP Publishing en 1742-6596 10.1088/1742-6596/490/1/012126 SHeidenreich S H LKlapp MBär article Heiden_PRL2013 Phys. Rev. Lett. 2013 110 228102 8.43, ActFluid 10.1103/PhysRevLett.110.228102 JDunkel SHeidenreich KDrescher H. HWensink MBär R. EGoldstein article Radszuweit2013 Phys. Rev. Lett. 2013 110 13 138102 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. Biological,Biomechanical Phenomena,Cell Physiological Phenomena,Cytoplasm,Cytoplasm: chemistry,Cytoskeleton,Cytoskeleton: chemistry,Elasticity,Extracellular Fluid,Extracellular Fluid: chemistry,Models,Viscosity 8.41, ActMatt, ActFluid http://www.ncbi.nlm.nih.gov/pubmed/23581377 1079-7114 10.1103/PhysRevLett.110.138102 MRadszuweit S.Alonso HEngel MBär article Dunkel2013 New J. Phys. 2013 15 4 045016 8.43, ActFluid http://iopscience.iop.org/article/10.1088/1367-2630/15/4/045016 IOP Publishing en 1367-2630 10.1088/1367-2630/15/4/045016 JDunkel SHeidenreich MBär R EGoldstein article Wensink2012 Proc. Natl. Acad. Sci. U.S.A. 2012 109 36 14308--13 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. Bacillus subtilis,Bacillus subtilis: physiology,Biological,Biomechanical Phenomena,Computer Simulation,Culture Media,Culture Media: chemistry,Hydrodynamics,Models,Movement,Movement: physiology 8.43, ActFluid http://www.pnas.org/content/109/36/14308 1091-6490 10.1073/pnas.1202032109 H HWensink JDunkel SHeidenreich KDrescher R EGoldstein HLöwen J MYeomans article Radszuweit2011 Eur. Phys. J. - Special Topics 2010 191 1 159--172 8.41,pattern formation 8.41, ActMatter, ActFluid http://www.springerlink.com/index/10.1140/epjst/e2010-01348-2 1951-6355 10.1140/epjst/e2010-01348-2 MRadszuweit HEngel MBär