08 Fakultät Mathematik und Physik
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Item Open Access Nichtlineare Halbgruppen und Hysteresemodelle für nichtmonotone Sättigungsprofile(2019) Steinle, Rouven; Hilfer, Rudolf (Prof. Dr. Dr.)Die experimentellen Beobachtungen von Sättigungsüberschüssen und Sättigungsfingern bei gravitationsgetriebenen Infiltrationsprozessen beschäftigt schon seit Jahrzehnten die Forschung von porösen Medien in Mathematik, Physik, Geowissenschaft und Ingenieurwesen. Sowohl die Vorhersage von Sättigungsüberschüssen bei Experimenten als auch das allgemeine theoretische Verständnis von Sättigungsüberschüssen ist noch nicht vollständig geklärt. Des Weiteren ist die Frage, ob Sättigungsüberschüsse und Sättigungsfinger eine Verbindung zueinander haben, weiterhin offen. Zur theoretischen Modellierung von nichtmonotonen Sättigungsprofilen und den Mechanismen, welche zur Entstehung und Ausbreitung dieser Profile nötig sind, gibt es eine Vielzahl von Ansätzen, beschrieben in Beliaev et al (Transport in Porous Media 43 (2001), S.487), Cuesta et al (European Journal of Applied Mathematics 11 (2000), S.381), Cueto-Felgueroso et al (Physical Review Letters 101 (2008), S.244504), DiCarlo et al (Transport in Porous Media 91 (2012), S.955), Doster et al (Physical Review E 86 (2012), S.016317) und Eliassi et al (Water Resources Research 38 (2002), S.1234). Ein Ansatz zur Ausbreitung von laufenden nichtmonotonen Sättigungsprofilen wurde von Hilfer und Steinle (The European Physical Journal Special Topics 223 (2014), S.2323) vorgestellt. Dieser Ansatz benutzt ausschließlich hysteretische relative Permeabilitäten zur Modellierung von Be- und Entwässerungsprozessen bei sich ausbreitenden Sättigungsüberschüssen. Sonstige Erweiterungen der Darcy-Theorie werden dabei nicht benutzt. Die Ausbreitungsgeschwindigkeiten der Sättigungsfronten werden mit einer Rankine-Hugoniot-Bedingung, welche die fraktionalen Flüsse verwendet, berechnet. Bei einer optimal aufeinander abgestimmten Wahl der relativen Permeabilitäten, der Material- und Fluidparameter sowie der Anfangs- und Randbedingungen, existieren Sättigungsüberschüsse, die sich mit konstanter Geschwindigkeit und konstanter Überschussbreite ausbreiten. In der vorliegenden Arbeit wird der Ansatz von Hilfer und Steinle (The European Physical Journal Special Topics 223 (2014), S.2323) auf die Darcy-Theorie in Verbindung mit einem allgemeinen Hysteresemodell mit graphenabhängigen relativen Permeabilitäten und Kapillardrücken angewendet. Das entstandene Anfangs- und Randwertproblem wird analytisch und numerisch untersucht. Im analytischen Teil wird sowohl das traditionelle als auch das hysteretische Anfangs- und Randwertproblem der Darcy-Theorie mit den Methoden der nichtlinearen Halbgruppentheorie diskutiert. Für die traditionelle Darcy-Theorie mit einer geeigneten Anfangsbedingung kann Existenz, Eindeutigkeit und Beschränktheit von Lösungen gezeigt werden. Darauf aufbauend werden diese Ergebnisse auf die hysteretische Darcy-Theorie angewendet. Im Rahmen einer vereinfachten Hystereseformulierung und mit geeigneten Bedingungen an die Anfangsbedingung und die Parameter der Gleichung existieren auch hier eindeutig Lösungen. Bei einer nichtmonotonen Anfangsbedingung sind diese Lösungen auch nichtmonoton. Des Weiteren wird die Ausbreitung von nichtmonotonen Sättigungsprofile mit Hilfe der Rankine-Hugoniot-Bedingung untersucht. Die Wahl der Parameter und Anfangs- und Randbedingungen erzeugt nicht nur laufende Sättigungsüberschüsse, sondern auch Überschüsse mit wachsender oder schrumpfender Plateaubreite. Nicht nur die Wahl der Parameter hat einen Einfluss auf die Ausbreitung der Lösungen, sondern auch die Wahl des Hysteresemodells. Abhängig vom Hysteresemodell, kann sich ein nichtmonotones Sättigungsprofil als laufende Welle oder mit wachsender oder schrumpfender Plateaubreite durch das poröse Medium bewegen. Außerdem kann man in der theoretischen Betrachtung nicht nur die Ausbreitung von Sättigungsüberschüssen bei schwerkraftgetriebenen, sondern auch bei horizontalen Strömungen erklären. Im numerischen Teil wird die hysteretische Darcy-Theorie für variierende Material- und Fluidparameter, Anfangs- und Randbedingungen und Hysteresemodelle untersucht. Die numerischen Simulationen bestätigen die analytischen Resultate und zeigen, dass die Lösungen unabhängig von der Hysterese im Kapillardruck und im kapillaren Fluss sind. Jedoch sind die Lösungen stark abhängig von den Anfangs- und Randwerten. In Folge dieser Abhängigkeit gibt es eine große Variation an qualitativ unterschiedlichen zeitlichen Entwicklungen der Sättigungsüberschüsse. Darüber hinaus werden existierende Experimente modelliert. Es kann gezeigt werden, dass die numerischen nichtmonotonen Sättigungsprofile mit den experimentellen Daten in Bezug auf Ausbreitungsgeschwindigkeiten, Überschussbreite und Überschusshöhe übereinstimmen. Des Weiteren wird numerisch untersucht, ob die Formulierung der Darcy-Theorie einen Einfluss auf die Lösungen hat. Bei einer geeigneten Wahl der Randbedingungen sind die numerischen Ergebnisse nahezu identischen und somit sind die Lösungen unabhängig von der Formulierung. Abschließend ist eine erste numerische Einordnung von Sättigungsfingern bei zweidimensionalen Strömungen möglich. Die numerischen Lösungen zeigen, dass nur ein Sättigungsfinger in Verbindung mit einem Sättigungsüberschuss in der Fingerspitze für lange Zeiten existiert. Diese Arbeit zeigt, dass die Beschreibung von laufenden Sättigungsüberschüssen im Rahmen der Darcy-Theorie mit hysteretischen relativen Permeabilitäten möglich ist. Zusätzlich zu laufenden Sättigungsüberschüssen existieren in der Theorie auch nichtlaufende nichtmonotone Sättigungsprofile mit wachsender oder schrumpfender Plateaubreite. Einerseits sind in der theoretischen Modellierung weitere Untersuchungen und numerische Simulationen für zweidimensionale Strömungen notwendig, um Aussagen über die Ausbreitung von Sättigungsfingern treffen zu können. Auf der anderen Seite sind auch weitere Forschungen mit längeren quasi-eindimensionalen porösen Medien notwendig, um herauszufinden, ob die nichtlaufenden Überschüsse aus der Theorie auch experimentell beobachtbar sind. Darüber hinaus wurden bei einer Kooperation mit dem Institut für Wasser- und Umweltsystemmodellierung (IWS) der Universität Stuttgart nichtmonotone Sättigungsprofile mit unterschiedlichen Implementierungen berechnet und verglichen, Schneider et al (Transport in Porous Media 121 (2018), Nr.3). Die numerischen Lösungen unterscheiden sich dabei nur minimal und damit konnte gezeigt werden, dass die Ausbreitung von Sättigungsüberschüssen nicht von der Wahl der numerischen Lösungsmethode abhängig ist.Item Open Access Molecular dynamics simulations for the study of interaction between non-canonical DNA structures and biochemically relevant co-solutes(2023) Oprzeska-Zingrebe, Ewa Anna; Smiatek, Jens (Priv.-Doz. Dr.)Non-canonical nucleic acid structures, such as DNA G-quadruplexes and i-Motifs, have been proved to play an important role in key biological processes, including gene expression, replication, regulation or telomere maintenance. The presence of G-quadruplexes in promoter regions of certain oncogenes turn them into a potential target for cancer therapies. Besides their biological implications, non-canonical DNA structures are present in genomes of various organisms, who adopt certain levels of co-solutes to protect their internal structures against the harsh environment. This study presents the research on the selected non-canonical DNA structures of particular biological relevance: G-quadruplex with only two tetrads, small DNA hairpin and ssDNA strand as well as canonical double helix. The atomistic molecular dynamics (MD) simulations have been applied to elucidate the structural, configuration and solvation properties of the analyzed structures in the presence of assorted co-solutes, composing the native cellular environment in nature: urea, ectoine and trimethylamine-N-oxide (TMAO). With the application of molecular theory of solutions, one determines and exemplifies the thermodynamic properties of investigated structures in various environments close to the physiological conditions present in living cells. This study uncovers the versatile nature of DNA interaction with diverse co-solutes and water, as well as the cross-interactions between the inorganic components of the biomolecular solution. The cellular mechanisms of DNA structural stabilization and destabilization are hereby described in terms of preferential binding and preferential exclusion, with particular emphasis on the properties of solvent structure within individual solvation shells. In this regards, this work presents a comprehensive study on the intracellular interactions involving nucleic acids, thus shedding light into their microscopic properties and opening the path for further biomedical research.Item Open Access Failure of granular assemblies(2011) Welker, Philipp; Hilfer, Rudolf (Appl. Prof. Dr. Dr.)This work investigates granular assemblies subjected to increasing external forces in the quasi-static limit. In this limit, the system’s evolution depends on static properties of the system, but is independent of the particles’ inertia. At the failure, which occurs at a certain value of the external forces, the particles’ motions increase quickly. In this thesis, the properties of granular systems during the weakening process and at the failure are investigated with the Discrete Element Method (DEM). Unlike continuum approaches, in the DEM each particle is represented by one element with certain properties. This method is combined with an analytical description and with numerical simulations of the granular systems. Although many results are obtained for systems with rigid boundaries in two dimensions, several aspects of granular behavior are investigated under different conditions: systems with rigid wall boundaries are compared to systems with membrane boundaries. Two and three dimensional systems with rigid wall boundaries show the dependence of weakening and failure on dimensionality. This enables one to separate the general granular behavior from individual trends. A comparison between two independently developed computer codes shows that the obtained results are a true physical property of our granular model, and are not due to a particular numerical procedure. The dependence of the results on the system size is a further important aspect. Since the size of a grain introduces a characteristic length, small systems and large systems behave differently. For some of the investigated properties, an average over many small systems is equal to the value of one large system, but this is not always the case. Thus the system size dependence of granular properties is nontrivial. This work investigates small systems with only 16 particles but also large systems with 16384 particles. Different aspects of granular behavior are investigated in different chapters. Chapter 1 introduces the reader to granular media, and Chap. 2 provides the theoretical framework for understanding the results in the following chapters. Chap. 3 considers the failure and triggers of failure in small systems with only 16 particles. This size is small enough to identify single particle contact changes and investigate their meaning for weakening and failure. The stability of the systems is calculated from the knowledge of the contact structure, i.e. from position and orientation of the contacts (geometric aspects) and their states (mechanical aspect). From this structure, the stiffness matrix is constructed, and a scalar stiffness is deduced. Changes in the stiffness can in this way be related to changes in the interparticle contact structure. A contact status change always appears at the beginning of the failure, decreasing the stiffness of the system. Thus, this contact status change is at the origin of failure. Through the change, the stiffness either becomes negative (instability), zero (null-mode motion), or very low. In the latter case the transition from a higher stiffness before the change to the low stiffness afterwards is rather slow. During the transition, a subsequent contact status change leads to the failure of the system. The results in Chap. 3 show that the stiffness matrix approach is successful in describing weakening and failure of granular systems. Thus Bagi’s definition of stability, which is based on the stiffness matrix description, is a useful concept for a more precise definition of jamming than the qualitative jamming diagram. In Chap. 4 the failure is investigated in more detail. Several publications show that there is a minimum number of interparticle contacts for which the system can stabilize the external forces at the boundaries. This limit, the so-called isostatic limit, defines the minimum number of contacts required for stability of a frictionless granular system. When friction comes into play, the counting of contacts becomes more complex: closed contacts contribute two stability conditions, and sliding contacts contribute one condition for stability. However, the results in Chap. 4 show that the failure of a granular system does not coincide with the minimum number of constraints required for stability, at least not based on the global comparison of constraints and degrees of freedom presented there. When a system fails, a shear band appears, where the particles’ kinetic energy is higher than elsewhere in the system. This immediately suggests evaluating the number of constraints in that region to be a promising route for refinement. Many aspects of the softening of granular systems on the way to the failure are explained in Chap. 5. The main result therein is that the softening of a granular assembly can be divided in two periods of different granular behavior. In the first period, many contacts become sliding, while in the second period the number of sliding contacts decreases. Also precursors of failure appear in the second period. They can be noticed as plunges in the number of sliding contacts, followed by a fast recovery. The evolution of sliding contacts can be fully understood in terms of contact status transitions. In the beginning of the simulation, most frequently a closed contact becomes a sliding contact. At the transition between the two periods, the number of sliding contacts becomes maximal. At this maximum, the inverse transition from sliding to closed is equally likely. Increasing the force further, another transition comes into play: sliding contacts disappear. This means the total number of contacts decreases. Finally, at the failure, all contact status transitions become equally likely. This behavior is a consequence of the global rearrangement involving a large number of grains. The spatial organization of sliding contacts also changes during the simulation. In the first period, sliding contacts tend to distribute evenly over the system, while they tend to cluster in the second period. This tendency increases until the failure, where the sliding contacts are finally concentrated in a diagonal band. Chapter 6 examines more closely the precursors mentioned in Chap. 5. These are localized instabilities, i.e. a negative local stiffness appears in the system. Consequently, the kinetic energy rises locally very quickly, and decreases again when, after a very short interval of time, stability is recovered. Due to the localization, the kinetic energy is much lower than at the failure. One can more easily identify precursors by the sudden plunge of the number of sliding contacts. This decrease is always temporary, and it can be understood in terms of contact status transitions: when a precursors appears, contacts become nonsliding in the region of the vibration wave, which is initiated by the precursor and radiated outward. When the vibration disappears, these contacts start to slide again. Changes in the contact structure are mainly transitional, therefore the importance of precursors for the internal structure is much smaller than the general trend, which depends on the external force. Chapter 7 examines closely the organization of motions, first observed in Chap. 5. While the system is stable, the two most important relative motions are the sliding of particles and the rolling of grains at their point of contact. This chapter shows that the latter motions do concentrate in bands appearing roughly at the angle pi/4 relative to the direction of increasing force. Such rolling bands were also observed by Kuhn and Bagi. The organization of rolling in bands increases as failure approaches. As the number of bands decreases, the distance between the rolling bands increases. Eventually only very few rolling bands remain, and one of them becomes the shear band which appears at the failure. Thus the rolling motions are concentrated within the shear band, contributing to the process of reorganization. The direction of the shear band found here is similar to the Mohr-Coulomb direction of failure. The latter is also obtained from the principle of least dissipation rate of Toeroek. Another important finding is the correlation of rolling and sliding motions. This correlation is stronger in the simulation beginning and at failure, and it is weaker at the maximum number of sliding contacts. Chapter 8 discusses the influence of the boundary conditions on the results presented in the foregoing chapters. Specifically, results obtained in systems with membrane boundaries are compared to results in systems with rigid wall boundaries. The comparison reveals that many details of the softening process and the failure are qualitatively independent of the boundary conditions. One example is the number of sliding contacts attaining a maximum before the failure, and disemboguing into a sharp maximum at the failure. The maximum always divides the softening process in two periods. On the contrary, the spatial organization of sliding contacts depends on the boundary conditions. Applying membrane boundary conditions leads to a constantly increasing clustering tendency with increasing force, which decreases again only at the failure of the system. When rigid walls boundaries are applied, sliding contacts tend to repel each other in the first period of the simulation, resulting in a more homogeneous distribution of sliding contacts. In the second period until the failure, sliding contacts show an increasing tendency to cluster. In both rigid walls and membrane conditions the sliding contacts concentrate at the failure in the shear band that develops. This suggests that the process of failure might be similar in both cases. A further important finding, explained in Chap. 9, is that the critical force at failure depends on the interparticle friction coefficient µ. When this coefficient is increased, the system fails at a higher value of the external force. A higher µ involves also a stronger decrease in the number of contacts M before failure, while the number of sliding contacts Ms involved in the weakening is lower. A very important finding is that while M and Ms vary considerably, the global hyperstatic number H observed at failure is almost independent of µ. This suggests that failure might be better characterized by µ-independent properties. Chapter 10 shows the behavior of granular systems in three dimensions. Applying similar boundary conditions as in two dimensions (rigid walls on every side of the system), important system characteristics can easily be compared. The comparison reveals that the approaching of failure in three dimensions is in some respects similar to two dimensions, but it has also some different features. One common observation is the initially linear increase in the number of sliding contacts ms. At the maximum ms, the behavior becomes different: ms decreases very quickly in three dimensions, while the decrease in two dimensions is smooth. The spatial organization of sliding contacts is also different: they always tend to cluster in three dimensions, while in two dimensions they only cluster in the second period before failure. Precursors are observed in both two and three dimensions. In both cases, their characteristics are similar, but their number is much higher in three dimensions. At least three main results can be distilled from this thesis. First, organization and clustering of sliding and rolling motions starts a long time before the failure is approached. Thus, in a macroscopic constitutive model, not only the number of sliding motions, but also their organization has to be taken into account. Second, precursors of the failure are always observed, independent of the boundary conditions and the dimensionality. In the literature, precursors of granular avalanches have been reported by several authors. The findings of this thesis show that the precursor phenomenon is more general and applies to rigid wall and membrane boundary conditions as well. Although from the limited number of examples it is impossible to draw a general conclusion, most probably precursors of failure occur for any kind of boundary conditions and for any load protocol. Third, the thesis provides new insight into the nature of failure: in small systems, failure is connected to the appearance of instability and an exponential rise in the kinetic energy. In large systems, vibrations, appearing at precursors, become larger close to failure. Thus the system explores an increasing part of phase space. These vibrations are physical, and not an artifact of the simulation: they appear in the same way after localized instabilities as they also do after the failure, when the system comes back to rest. These vibrations are important for failure in large systems. This importance might trigger future investigations of granular media. What are the perspectives for future work? First, the global hyperstatic number H, defined in Sec. 2.7 and investigated in Sec. 4.1, could be locally defined. The hyperstatic number compares the number of constraints with the number of degrees of freedom. The refinement to a local definition is promising because sliding and rolling motions organize in localized diagonal bands close to failure. Thus failure might be a local happening, and calculating H in these regions might give further insight to what precisely happens at failure. For example, the mystery of failure being approximately an isostatic transition (H = 0) in small systems, but hyperstatic (H > 0) in large systems, could probably be explained by this approach: the isostatic region might be localized. Second, the number of precursors could be counted for each type of boundary conditions, and the rise in this number until failure could be evaluated. Also the position of subsequent precursors could be related to each other. Are the positions correlated? This would be interesting to know. Note that for this purpose it would be advisable to control the boundary motions (i.e. the strain) instead of the external forces (i.e. the stress). This increases the resolution close to the failure, where most precursors occur. Last but not least, a few more words about the jamming diagram, introduced in Fig. 1.1 should be said, linking the results of this thesis with this diagram. Granular systems belong generally to the blue plane in the jamming diagram, defined by the density and the external force, which is the load. Considering the systems here, at least one more parameter must be introduced to fully pin the shaded jamming surface. This parameter is the interparticle friction coefficient µ. When it is reduced, the maximum supported load decreases. As the results in Chap. 9 show, the type of failure transition also changes qualitatively from µ = 0 to µ = infinity (See Fig. 9.1). For small µ, the hyperstatic number H, which reflects the number of stabilizing contact forces, evolves smoothly and continuously at the failure. For µ > 0.3, this number plunges suddenly at the failure. If the simulations are not quasi-static, the parameter load protocol must also be added to the list, because failure appears at a higher load when the external force is quickly increased. In the jamming diagram, the precise meaning of the axis load is also not clear. Most probably the authors mean a deviator stress which is applied to the system. This would be a good specification, because failure is most frequently identified with the point of maximum deviator stress. However, the maximum stress might depend on the dimensionality. Consequently the jamming surface in the diagram proposed by Liu and Nagel is only unique when a specific set of parameters is chosen. But then the same set of parameters must be applied to all systems (i.e. to grains, bubbles, glasses). Further investigation is needed to identify if the jamming diagram in the proposed form relates the granular failure to the glass transition in a favorable and unique way.