@article{GiewekemeyerKruegerKalbfleischetal.2011,
  author    = {Giewekemeyer, K. and Krueger, S. P. and Kalbfleisch, S. and Bartels, Meike and Beta, Carsten and Salditt, T.},
  title     = {X-ray propagation microscopy of biological cells using waveguides as a quasipoint source},
  series = {Physical review : A, Atomic, molecular, and optical physics},
  volume    = {83},
  journal   = {Physical review : A, Atomic, molecular, and optical physics},
  number    = {2},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1050-2947},
  doi       = {10.1103/PhysRevA.83.023804},
  pages     = {7},
  year      = {2011},
  abstract  = {We have used x-ray waveguides as highly confining optical elements for nanoscale imaging of unstained biological cells using the simple geometry of in-line holography. The well-known twin-image problem is effectively circumvented by a simple and fast iterative reconstruction. The algorithm which combines elements of the classical Gerchberg-Saxton scheme and the hybrid-input-output algorithm is optimized for phase-contrast samples, well-justified for imaging of cells at multi-keV photon energies. The experimental scheme allows for a quantitative phase reconstruction from a single holographic image without detailed knowledge of the complex illumination function incident on the sample, as demonstrated for freeze-dried cells of the eukaryotic amoeba Dictyostelium discoideum. The accessible resolution range is explored by simulations, indicating that resolutions on the order of 20 nm are within reach applying illumination times on the order of minutes at present synchrotron sources.},
  language  = {en}
}
@misc{BetaGovYochelis2020,
  author    = {Beta, Carsten and Gov, Nir S. and Yochelis, Arik},
  title     = {Why a Large-Scale Mode Can Be Essential for Understanding Intracellular Actin Waves},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {967},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47358},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-473588},
  pages     = {20},
  year      = {2020},
  abstract  = {During the last decade, intracellular actin waves have attracted much attention due to their essential role in various cellular functions, ranging from motility to cytokinesis. Experimental methods have advanced significantly and can capture the dynamics of actin waves over a large range of spatio-temporal scales. However, the corresponding coarse-grained theory mostly avoids the full complexity of this multi-scale phenomenon. In this perspective, we focus on a minimal continuum model of activator-inhibitor type and highlight the qualitative role of mass conservation, which is typically overlooked. Specifically, our interest is to connect between the mathematical mechanisms of pattern formation in the presence of a large-scale mode, due to mass conservation, and distinct behaviors of actin waves.},
  language  = {en}
}
@article{BetaGovYochelis2020,
  author    = {Beta, Carsten and Gov, Nir S. and Yochelis, Arik},
  title     = {Why a Large-Scale Mode Can Be Essential for Understanding Intracellular Actin Waves},
  series = {Cells},
  volume    = {9},
  journal   = {Cells},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4409},
  doi       = {10.3390/cells9061533},
  pages     = {18},
  year      = {2020},
  abstract  = {During the last decade, intracellular actin waves have attracted much attention due to their essential role in various cellular functions, ranging from motility to cytokinesis. Experimental methods have advanced significantly and can capture the dynamics of actin waves over a large range of spatio-temporal scales. However, the corresponding coarse-grained theory mostly avoids the full complexity of this multi-scale phenomenon. In this perspective, we focus on a minimal continuum model of activator-inhibitor type and highlight the qualitative role of mass conservation, which is typically overlooked. Specifically, our interest is to connect between the mathematical mechanisms of pattern formation in the presence of a large-scale mode, due to mass conservation, and distinct behaviors of actin waves.},
  language  = {en}
}
@article{VilkAghionAvgaretal.2022,
  author    = {Vilk, Ohad and Aghion, Erez and Avgar, Tal and Beta, Carsten and Nagel, Oliver and Sabri, Adal and Sarfati, Raphael and Schwartz, Daniel K. and Weiß, Matthias and Krapf, Diego and Nathan, Ran and Metzler, Ralf and Assaf, Michael},
  title     = {Unravelling the origins of anomalous diffusion},
  series = {Physical Review Research},
  volume    = {4},
  journal   = {Physical Review Research},
  number    = {3},
  publisher = {American Physical Society},
  address   = {College Park, MD},
  issn      = {2643-1564},
  doi       = {10.1103/PhysRevResearch.4.033055},
  pages     = {033055-1 -- 033055-16},
  year      = {2022},
  abstract  = {Anomalous diffusion or, more generally, anomalous transport, with nonlinear dependence of the mean-squared displacement on the measurement time, is ubiquitous in nature. It has been observed in processes ranging from microscopic movement of molecules to macroscopic, large-scale paths of migrating birds. Using data from multiple empirical systems, spanning 12 orders of magnitude in length and 8 orders of magnitude in time, we employ a method to detect the individual underlying origins of anomalous diffusion and transport in the data. This method decomposes anomalous transport into three primary effects: long-range correlations ("Joseph effect"), fat-tailed probability density of increments ("Noah effect"), and nonstationarity ("Moses effect"). We show that such a decomposition of real-life data allows us to infer nontrivial behavioral predictions and to resolve open questions in the fields of single-particle tracking in living cells and movement ecology.},
  language  = {en}
}
@misc{VilkAghionAvgaretal.2022,
  author    = {Vilk, Ohad and Aghion, Erez and Avgar, Tal and Beta, Carsten and Nagel, Oliver and Sabri, Adal and Sarfati, Raphael and Schwartz, Daniel K. and Weiß, Matthias and Krapf, Diego and Nathan, Ran and Metzler, Ralf and Assaf, Michael},
  title     = {Unravelling the origins of anomalous diffusion},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1303},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-57764},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-577643},
  pages     = {16},
  year      = {2022},
  abstract  = {Anomalous diffusion or, more generally, anomalous transport, with nonlinear dependence of the mean-squared displacement on the measurement time, is ubiquitous in nature. It has been observed in processes ranging from microscopic movement of molecules to macroscopic, large-scale paths of migrating birds. Using data from multiple empirical systems, spanning 12 orders of magnitude in length and 8 orders of magnitude in time, we employ a method to detect the individual underlying origins of anomalous diffusion and transport in the data. This method decomposes anomalous transport into three primary effects: long-range correlations ("Joseph effect"), fat-tailed probability density of increments ("Noah effect"), and nonstationarity ("Moses effect"). We show that such a decomposition of real-life data allows us to infer nontrivial behavioral predictions and to resolve open questions in the fields of single-particle tracking in living cells and movement ecology.},
  language  = {en}
}
@article{Beta2016,
  author    = {Beta, Carsten},
  title     = {To turn or not to turn?},
  series = {NEW JOURNAL OF PHYSICS},
  volume    = {18},
  journal   = {NEW JOURNAL OF PHYSICS},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/18/5/051003},
  pages     = {1 -- 17},
  year      = {2016},
  abstract  = {Bacteria typically swim in straight runs, interruped by sudden turning events. In particular, some species are limited to a reversal in the swimming direction as the only turning maneuver at their disposal. In a recent article, Grossmann et al (2016 New J. Phys. 18 043009) introduce a theoretical framework to analyze the diffusive properties of active particles following this type of run-and-reverse pattern. Based on a stochastic clock model to mimic the regulatory pathway that triggers reversal events, they show that a run-and-reverse swimmer can optimize its diffusive spreading by tuning the reversal rate according to the level of rotational noise. With their approach, they open up promising new perspectives of how to incorporate the dynamics of intracellular signaling into coarse-grained active particle descriptions.},
  language  = {en}
}
@misc{StichBeta2019,
  author    = {Stich, Michael and Beta, Carsten},
  title     = {Time-Delay Feedback Control of an Oscillatory Medium},
  series = {Biological Systems: Nonlinear Dynamics Approach},
  volume    = {20},
  journal   = {Biological Systems: Nonlinear Dynamics Approach},
  publisher = {Springer},
  address   = {Cham},
  isbn      = {978-3-030-16585-7},
  issn      = {2199-3041},
  doi       = {10.1007/978-3-030-16585-7_1},
  pages     = {1 -- 17},
  year      = {2019},
  abstract  = {The supercritical Hopf bifurcation is one of the simplest ways in which a stationary state of a nonlinear system can undergo a transition to stable self-sustained oscillations. At the bifurcation point, a small-amplitude limit cycle is born, which already at onset displays a finite frequency. If we consider a reaction-diffusion system that undergoes a supercritical Hopf bifurcation, its dynamics is described by the complex Ginzburg-Landau equation (CGLE). Here, we study such a system in the parameter regime where the CGLE shows spatio-temporal chaos. We review a type of time-delay feedback methods which is suitable to suppress chaos and replace it by other spatio-temporal solutions such as uniform oscillations, plane waves, standing waves, and the stationary state.},
  language  = {en}
}
@article{RaatzHintscheBahrsetal.2015,
  author    = {Raatz, Michael and Hintsche, Marius and Bahrs, Marco and Theves, Matthias and Beta, Carsten},
  title     = {Swimming patterns of a polarly flagellated bacterium in environments of increasing complexity},
  series = {European physical journal special topics},
  volume    = {224},
  journal   = {European physical journal special topics},
  number    = {7},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1951-6355},
  doi       = {10.1140/epjst/e2015-02454-3},
  pages     = {1185 -- 1198},
  year      = {2015},
  abstract  = {The natural habitat of many bacterial swimmers is dominated by interfaces and narrow interstitial spacings where they frequently interact with the fluid boundaries in their vicinity. To quantify these interactions, we investigated the swimming behavior of the soil bacterium Pseudomonas putida in a variety of confined environments. Using microfluidic techniques, we fabricated structured microchannels with different configurations of cylindrical obstacles. In these environments, we analyzed the swimming trajectories for different obstacle densities and arrangements. Although the overall swimming pattern remained similar to movement in the bulk fluid, we observed a change in the turning angle distribution that could be attributed to collisions with the cylindrical obstacles. Furthermore, a comparison of the mean run length of the bacteria to the mean free path of a billiard particle in the same geometry indicated that, inside a densely packed environment, the trajectories of the bacterial swimmers are efficiently guided along the open spacings.},
  language  = {en}
}
@misc{SeyrichAlirezaeizanjaniBetaetal.2018,
  author    = {Seyrich, Maximilian and Alirezaeizanjani, Zahra and Beta, Carsten and Stark, Holger},
  title     = {Statistical parameter inference of bacterial swimming strategies},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {914},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44621},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-446214},
  pages     = {23},
  year      = {2018},
  abstract  = {We provide a detailed stochastic description of the swimming motion of an E. coli bacterium in two dimension, where we resolve tumble events in time. For this purpose, we set up two Langevin equations for the orientation angle and speed dynamics. Calculating moments, distribution and autocorrelation functions from both Langevin equations and matching them to the same quantities determined from data recorded in experiments, we infer the swimming parameters of E. coli. They are the tumble rate lambda, the tumble time r(-1), the swimming speed v(0), the strength of speed fluctuations sigma, the relative height of speed jumps eta, the thermal value for the rotational diffusion coefficient D-0, and the enhanced rotational diffusivity during tumbling D-T. Conditioning the observables on the swimming direction relative to the gradient of a chemoattractant, we infer the chemotaxis strategies of E. coli. We confirm the classical strategy of a lower tumble rate for swimming up the gradient but also a smaller mean tumble angle (angle bias). The latter is realized by shorter tumbles as well as a slower diffusive reorientation. We also find that speed fluctuations are increased by about 30\% when swimming up the gradient compared to the reversed direction.},
  language  = {en}
}
@article{SeyrichAlirezaeizanjaniBetaetal.2018,
  author    = {Seyrich, Maximilian and Alirezaeizanjani, Zahra and Beta, Carsten and Stark, Holger},
  title     = {Statistical parameter inference of bacterial swimming strategies},
  series = {New journal of physics : the open-access journal for physics},
  volume    = {20},
  journal   = {New journal of physics : the open-access journal for physics},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1367-2630},
  doi       = {10.1088/1367-2630/aae72c},
  pages     = {20},
  year      = {2018},
  abstract  = {We provide a detailed stochastic description of the swimming motion of an E. coli bacterium in two dimension, where we resolve tumble events in time. For this purpose, we set up two Langevin equations for the orientation angle and speed dynamics. Calculating moments, distribution and autocorrelation functions from both Langevin equations and matching them to the same quantities determined from data recorded in experiments, we infer the swimming parameters of E. coli. They are the tumble rate lambda, the tumble time r(-1), the swimming speed v(0), the strength of speed fluctuations sigma, the relative height of speed jumps eta, the thermal value for the rotational diffusion coefficient D-0, and the enhanced rotational diffusivity during tumbling D-T. Conditioning the observables on the swimming direction relative to the gradient of a chemoattractant, we infer the chemotaxis strategies of E. coli. We confirm the classical strategy of a lower tumble rate for swimming up the gradient but also a smaller mean tumble angle (angle bias). The latter is realized by shorter tumbles as well as a slower diffusive reorientation. We also find that speed fluctuations are increased by about 30\% when swimming up the gradient compared to the reversed direction.},
  language  = {en}
}