@phdthesis{Breuer2016,
  author    = {Breuer, David},
  title     = {The plant cytoskeleton as a transportation network},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93583},
  school      = {Universit{\"a}t Potsdam},
  pages     = {164},
  year      = {2016},
  abstract  = {The cytoskeleton is an essential component of living cells. It is composed of different types of protein filaments that form complex, dynamically rearranging, and interconnected networks. The cytoskeleton serves a multitude of cellular functions which further depend on the cell context. In animal cells, the cytoskeleton prominently shapes the cell's mechanical properties and movement. In plant cells, in contrast, the presence of a rigid cell wall as well as their larger sizes highlight the role of the cytoskeleton in long-distance intracellular transport. As it provides the basis for cell growth and biomass production, cytoskeletal transport in plant cells is of direct environmental and economical relevance. However, while knowledge about the molecular details of the cytoskeletal transport is growing rapidly, the organizational principles that shape these processes on a whole-cell level remain elusive. This thesis is devoted to the following question: How does the complex architecture of the plant cytoskeleton relate to its transport functionality? The answer requires a systems level perspective of plant cytoskeletal structure and transport. To this end, I combined state-of-the-art confocal microscopy, quantitative digital image analysis, and mathematically powerful, intuitively accessible graph-theoretical approaches. This thesis summarizes five of my publications that shed light on the plant cytoskeleton as a transportation network: (1) I developed network-based frameworks for accurate, automated quantification of cytoskeletal structures, applicable in, e.g., genetic or chemical screens; (2) I showed that the actin cytoskeleton displays properties of efficient transport networks, hinting at its biological design principles; (3) Using multi-objective optimization, I demonstrated that different plant cell types sustain cytoskeletal networks with cell-type specific and near-optimal organization; (4) By investigating actual transport of organelles through the cell, I showed that properties of the actin cytoskeleton are predictive of organelle flow and provided quantitative evidence for a coordination of transport at a cellular level; (5) I devised a robust, optimization-based method to identify individual cytoskeletal filaments from a given network representation, allowing the investigation of single filament properties in the network context. The developed methods were made publicly available as open-source software tools. Altogether, my findings and proposed frameworks provide quantitative, system-level insights into intracellular transport in living cells. Despite my focus on the plant cytoskeleton, the established combination of experimental and theoretical approaches is readily applicable to different organisms. Despite the necessity of detailed molecular studies, only a complementary, systemic perspective, as presented here, enables both understanding of cytoskeletal function in its evolutionary context as well as its future technological control and utilization.},
  language  = {en}
}
@misc{Beta2010,
  author    = {Beta, Carsten},
  title     = {Bistability in the actin cortex},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  volume    = {3},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {12},
  doi       = {10.25932/publishup-42938},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-429385},
  pages     = {9},
  year      = {2010},
  abstract  = {Multi-color fluorescence imaging experiments of wave forming Dictyostelium cells have revealed that actin waves separate two domains of the cell cortex that differ in their actin structure and phosphoinositide composition. We propose a bistable model of actin dynamics to account for these experimental observation. The model is based on the simplifying assumption that the actin cytoskeleton is composed of two distinct network types, a dendritic and a bundled network. The two structurally different states that were observed in experiments correspond to the stable fixed points in the bistable regime of this model. Each fixed point is dominated by one of the two network types. The experimentally observed actin waves can be considered as trigger waves that propagate transitions between the two stable fixed points.},
  language  = {en}
}
@phdthesis{Krohmer2016,
  author    = {Krohmer, Anton},
  title     = {Structures \& algorithms in hyperbolic random graphs},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-395974},
  school      = {Universit{\"a}t Potsdam},
  pages     = {xii, 102},
  year      = {2016},
  abstract  = {Complex networks are ubiquitous in nature and society. They appear in vastly different domains, for instance as social networks, biological interactions or communication networks. Yet in spite of their different origins, these networks share many structural characteristics. For instance, their degree distribution typically follows a power law. This means that the fraction of vertices of degree k is proportional to k^(-β) for some constant β; making these networks highly inhomogeneous. Furthermore, they also typically have high clustering, meaning that links between two nodes are more likely to appear if they have a neighbor in common. To mathematically study the behavior of such networks, they are often modeled as random graphs. Many of the popular models like inhomogeneous random graphs or Preferential Attachment excel at producing a power law degree distribution. Clustering, on the other hand, is in these models either not present or artificially enforced. Hyperbolic random graphs bridge this gap by assuming an underlying geometry to the graph: Each vertex is assigned coordinates in the hyperbolic plane, and two vertices are connected if they are nearby. Clustering then emerges as a natural consequence: Two nodes joined by an edge are close by and therefore have many neighbors in common. On the other hand, the exponential expansion of space in the hyperbolic plane naturally produces a power law degree sequence. Due to the hyperbolic geometry, however, rigorous mathematical treatment of this model can quickly become mathematically challenging. In this thesis, we improve upon the understanding of hyperbolic random graphs by studying its structural and algorithmical properties. Our main contribution is threefold. First, we analyze the emergence of cliques in this model. We find that whenever the power law exponent β is 2 < β < 3, there exists a clique of polynomial size in n. On the other hand, for β >= 3, the size of the largest clique is logarithmic; which severely contrasts previous models with a constant size clique in this case. We also provide efficient algorithms for finding cliques if the hyperbolic node coordinates are known. Second, we analyze the diameter, i. e., the longest shortest path in the graph. We find that it is of order O(polylog(n)) if 2 < β < 3 and O(logn) if β > 3. To complement these findings, we also show that the diameter is of order at least Ω(logn). Third, we provide an algorithm for embedding a real-world graph into the hyperbolic plane using only its graph structure. To ensure good quality of the embedding, we perform extensive computational experiments on generated hyperbolic random graphs. Further, as a proof of concept, we embed the Amazon product recommendation network and observe that products from the same category are mapped close together.},
  language  = {en}
}