@phdthesis{Ullner2004,
  author    = {Ullner, Ekkehard},
  title     = {Noise-induced phenomena of signal transmission in excitable neural models},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0001522},
  school      = {Universit{\"a}t Potsdam},
  year      = {2004},
  abstract  = {Meine Dissertation behandelt verschiedene neue rauschinduzierte Ph{\"a}nomene in anregbaren Neuronenmodellen, insbesondere solche mit FitzHugh-Nagumo Dynamik. Ich beschreibe das Auftreten von vibronischer Resonanz in anregbaren Systemen. Sowohl in einer anregbaren elektronischen Schaltung als auch im FitzHugh-Nagumo Modell zeige ich, daß eine optimale Amplitude einer hochfrequenten externen Kraft die Signalantwort bez{\"u}glich eines niederfrequenten Signals verbessert. Weiterhin wird der Einfluß von additivem Rauschen auf das Zusammenwirken von stochastischer und vibronischer Resonanz untersucht. Weiterhin untersuche ich Systeme, die sowohl oszillierende als auch anregbare Eigenschaften beinhalten und dadurch zwei interne Frequenzen aufweisen. Ich zeige, daß in solchen Systemen der Effekt der stochastischen Resonanz deutlich erh{\"o}ht werden kann, wenn eine zus{\"a}tzliche hochfrequente Kraft in Resonanz mit den kleinen Oszillationen unterhalb der Anregungsschwelle hinzugenommen wird. Es ist beachtenswert, daß diese Verst{\"a}rkung der stochastischen Resonanz eine geringere Rauschintensit{\"a}t zum Erreichen des Optimums ben{\"o}tigt als die standartm{\"a}ßige stochastische Resonanz in anregbaren Systemen. Ich untersuche Frequenzselektivit{\"a}t bei der rauschinduzierten Signalverarbeitung von Signalen unterhalb der Anregungsschwelle in Systemen mit vielen rauschunterst{\"u}tzten stochastischen Attraktoren. Diese neuen Attraktoren mit abweichenden gemittelten Perioden weisen auch unterschiedliche Phasenbeziehungen zwischen den einzelnen Elementen auf. Ich zeige, daß die Signalantwort des gekoppelten Systems unter verschiedenen Rauscheinwirkungen deutlich verbessert oder auch reduziert werden kann durch das Treiben einzelner Elemente in Resonanz mit diesen neuen Resonanzfrequenzen, die mit passenden Phasenbeziehungen korrespondieren. Weiterhin konnte ich einen rauschinduzierten Phasen{\"u}bergang von einem selbstoszillierenden System zu einem anregbaren System nachweisen. Dieser {\"U}bergang erfolgt durch eine rauschinduzierte Stabilisierung eines deterministisch instabilen Fixpunktes der lokalen Dynamik, w{\"a}hrend die gesamte Phasenraumstruktur des Systems erhalten bleibt. Die gemeinsame Wirkung von Kopplung und Rauschen f{\"u}hrt zu einem neuen Typ von Phasen{\"u}berg{\"a}ngen und bewirkt eine Stabilisierung des Systems. Das sich daraus ergebende rauschinduziert anregbare Regime zeigt charakteristische Eigenschaften von klassisch anregbaren Systemen, wie stochastische Resonanz und Wellenausbreitung. Dieser rauschinduzierte Phasen{\"u}bergang erm{\"o}glicht dadurch die {\"U}bertragung von Signalen durch ansonsten global oszillierende Systeme und die Kontrolle der Signal{\"u}bertragung durch Ver{\"a}nderung der Rauschintensit{\"a}t. Insbesondere er{\"o}ffnen diese theoretischen Ergebnisse einen m{\"o}glichen Mechanismus zur Unterdr{\"u}ckung unerw{\"u}nschter globaler Oszillationen in neuronalen Netzwerken, welche charakteristisch f{\"u}r abnorme medizinische Zust{\"a}nde, wie z.B. bei der Parkinson\′schen Krankheit oder Epilepsie, sind. Die Wirkung von Rauschen w{\"u}rde dann wieder die Anregbarkeit herstellen, die den normalen Zustand der erkrankten Neuronen darstellt.},
  language  = {en}
}
@phdthesis{Niedermayer2012,
  author    = {Niedermayer, Thomas},
  title     = {On the depolymerization of actin filaments},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-63605},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Actin is one of the most abundant and highly conserved proteins in eukaryotic cells. The globular protein assembles into long filaments, which form a variety of different networks within the cytoskeleton. The dynamic reorganization of these networks - which is pivotal for cell motility, cell adhesion, and cell division - is based on cycles of polymerization (assembly) and depolymerization (disassembly) of actin filaments. Actin binds ATP and within the filament, actin-bound ATP is hydrolyzed into ADP on a time scale of a few minutes. As ADP-actin dissociates faster from the filament ends than ATP-actin, the filament becomes less stable as it grows older. Recent single filament experiments, where abrupt dynamical changes during filament depolymerization have been observed, suggest the opposite behavior, however, namely that the actin filaments become increasingly stable with time. Several mechanisms for this stabilization have been proposed, ranging from structural transitions of the whole filament to surface attachment of the filament ends. The key issue of this thesis is to elucidate the unexpected interruptions of depolymerization by a combination of experimental and theoretical studies. In new depolymerization experiments on single filaments, we confirm that filaments cease to shrink in an abrupt manner and determine the time from the initiation of depolymerization until the occurrence of the first interruption. This duration differs from filament to filament and represents a stochastic variable. We consider various hypothetical mechanisms that may cause the observed interruptions. These mechanisms cannot be distinguished directly, but they give rise to distinct distributions of the time until the first interruption, which we compute by modeling the underlying stochastic processes. A comparison with the measured distribution reveals that the sudden truncation of the shrinkage process neither arises from blocking of the ends nor from a collective transition of the whole filament. Instead, we predict a local transition process occurring at random sites within the filament. The combination of additional experimental findings and our theoretical approach confirms the notion of a local transition mechanism and identifies the transition as the photo-induced formation of an actin dimer within the filaments. Unlabeled actin filaments do not exhibit pauses, which implies that, in vivo, older filaments become destabilized by ATP hydrolysis. This destabilization can be identified with an acceleration of the depolymerization prior to the interruption. In the final part of this thesis, we theoretically analyze this acceleration to infer the mechanism of ATP hydrolysis. We show that the rate of ATP hydrolysis is constant within the filament, corresponding to a random as opposed to a vectorial hydrolysis mechanism.},
  language  = {en}
}
@phdthesis{Mueller2008,
  author    = {M{\"u}ller, Melanie J. I.},
  title     = {Bidirectional transport by molecular motors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18715},
  school      = {Universit{\"a}t Potsdam},
  year      = {2008},
  abstract  = {In biological cells, the long-range intracellular traffic is powered by molecular motors which transport various cargos along microtubule filaments. The microtubules possess an intrinsic direction, having a 'plus' and a 'minus' end. Some molecular motors such as cytoplasmic dynein walk to the minus end, while others such as conventional kinesin walk to the plus end. Cells typically have an isopolar microtubule network. This is most pronounced in neuronal axons or fungal hyphae. In these long and thin tubular protrusions, the microtubules are arranged parallel to the tube axis with the minus ends pointing to the cell body and the plus ends pointing to the tip. In such a tubular compartment, transport by only one motor type leads to 'motor traffic jams'. Kinesin-driven cargos accumulate at the tip, while dynein-driven cargos accumulate near the cell body. We identify the relevant length scales and characterize the jamming behaviour in these tube geometries by using both Monte Carlo simulations and analytical calculations. A possible solution to this jamming problem is to transport cargos with a team of plus and a team of minus motors simultaneously, so that they can travel bidirectionally, as observed in cells. The presumably simplest mechanism for such bidirectional transport is provided by a 'tug-of-war' between the two motor teams which is governed by mechanical motor interactions only. We develop a stochastic tug-of-war model and study it with numerical and analytical calculations. We find a surprisingly complex cooperative motility behaviour. We compare our results to the available experimental data, which we reproduce qualitatively and quantitatively.},
  language  = {en}
}
@phdthesis{Berger2012,
  author    = {Berger, Florian},
  title     = {Different modes of cooperative transport by molecular motors},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-60319},
  school      = {Universit{\"a}t Potsdam},
  year      = {2012},
  abstract  = {Cargo transport by molecular motors is ubiquitous in all eukaryotic cells and is typically driven cooperatively by several molecular motors, which may belong to one or several motor species like kinesin, dynein or myosin. These motor proteins transport cargos such as RNAs, protein complexes or organelles along filaments, from which they unbind after a finite run length. Understanding how these motors interact and how their movements are coordinated and regulated is a central and challenging problem in studies of intracellular transport. In this thesis, we describe a general theoretical framework for the analysis of such transport processes, which enables us to explain the behavior of intracellular cargos based on the transport properties of individual motors and their interactions. Motivated by recent in vitro experiments, we address two different modes of transport: unidirectional transport by two identical motors and cooperative transport by actively walking and passively diffusing motors. The case of cargo transport by two identical motors involves an elastic coupling between the motors that can reduce the motors' velocity and/or the binding time to the filament. We show that this elastic coupling leads, in general, to four distinct transport regimes. In addition to a weak coupling regime, kinesin and dynein motors are found to exhibit a strong coupling and an enhanced unbinding regime, whereas myosin motors are predicted to attain a reduced velocity regime. All of these regimes, which we derive both by analytical calculations and by general time scale arguments, can be explored experimentally by varying the elastic coupling strength. In addition, using the time scale arguments, we explain why previous studies came to different conclusions about the effect and relevance of motor-motor interference. In this way, our theory provides a general and unifying framework for understanding the dynamical behavior of two elastically coupled molecular motors. The second mode of transport studied in this thesis is cargo transport by actively pulling and passively diffusing motors. Although these passive motors do not participate in active transport, they strongly enhance the overall cargo run length. When an active motor unbinds, the cargo is still tethered to the filament by the passive motors, giving the unbound motor the chance to rebind and continue its active walk. We develop a stochastic description for such cooperative behavior and explicitly derive the enhanced run length for a cargo transported by one actively pulling and one passively diffusing motor. We generalize our description to the case of several pulling and diffusing motors and find an exponential increase of the run length with the number of involved motors.},
  language  = {en}
}
@phdthesis{Ahlers2001,
  author    = {Ahlers, Volker},
  title     = {Scaling and synchronization in deterministic and stochastic nonlinear dynamical systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-0000320},
  school      = {Universit{\"a}t Potsdam},
  year      = {2001},
  abstract  = {Gegenstand dieser Arbeit ist die Untersuchung universeller Skalengesetze, die in gekoppelten chaotischen Systemen beobachtet werden. Ergebnisse werden erzielt durch das Ersetzen der chaotischen Fluktuationen in der St{\"o}rungsdynamik durch stochastische Prozesse. Zun{\"a}chst wird ein zeitkontinuierliches stochastisches Modell f{\"u}rschwach gekoppelte chaotische Systeme eingef{\"u}hrt, um die Skalierung der Lyapunov-Exponenten mit der Kopplungsst{\"a}rke (coupling sensitivity of chaos) zu untersuchen. Mit Hilfe der Fokker-Planck-Gleichung werden Skalengesetze hergeleitet, die von Ergebnissen numerischer Simulationen best{\"a}tigt werden. Anschließend wird der neuartige Effekt der vermiedenen Kreuzung von Lyapunov-Exponenten schwach gekoppelter ungeordneter chaotischer Systeme beschrieben, der qualitativ der Abstoßung zwischen Energieniveaus in Quantensystemen {\"a}hnelt. Unter Benutzung der f{\"u}r die coupling sensitivity of chaos gewonnenen Skalengesetze wird ein asymptotischer Ausdruck f{\"u}r die Verteilungsfunktion kleiner Abst{\"a}nde zwischen Lyapunov-Exponenten hergeleitet und mit Ergebnissen numerischer Simulationen verglichen. Schließlich wird gezeigt, dass der Synchronisations{\"u}bergang in starkgekoppelten r{\"a}umlich ausgedehnten chaotischen Systemen einem kontinuierlichen Phasen{\"u}bergang entspricht, mit der Kopplungsst{\"a}rke und dem Synchronisationsfehler als Kontroll- beziehungsweise Ordnungsparameter. Unter Benutzung von Ergebnissen numerischer Simulationen sowie theoretischen {\"U}berlegungen anhand einer partiellen Differentialgleichung mit multiplikativem Rauschen werden die Universalit{\"a}tsklassen der zwei beobachteten {\"U}bergangsarten bestimmt (Kardar-Parisi-Zhang-Gleichung mit S{\"a}ttigungsterm, gerichtete Perkolation).},
  language  = {en}
}