The dynamics of chemically active droplets

In unserem täglichen Leben begegnen wir Tropfen oft in physikalischen Systems, beispielsweise als Öltropfen in Salatsoße. Diese Tropfen sind meist chemisch inaktiv. In biologischen Zellen bilden Proteine und RNA zusammen Tropfen. Zellen sind chemisch aktiv, so dass die Tropfenkomponenten neu gebildet, abgebaut und modifiziert werden können. In dieser Doktorarbeit wird das dynamische Verhalten von chemisch aktiven Tropfen mit analytischen und numerischen Methoden untersucht. Um das dynamische Verhalten von solchen aktiven Tropfen zu untersuchen, benutzen wir ein Minimalmodell mit zwei Komponenten, die zwei Phasen bilden und durch chemische Reaktionen ineinander umgewandelt werden. Die chemischen Reaktionen werden durch das Brechen von Detailed Balance aus dem Gleichgewicht gehalten, so dass die Tropfen chemisch aktiv sind. Wir konzentrieren uns auf den Fall, in dem Tropfenmaterial im Tropfen in die äußere Komponente umgewandelt wird, und in der äußeren Phase erzeugt wird. Wir finden ein vielfältiges dynamisches Phasendiagramm mit Regionen, in denen Tropfen schrumpfen und verschwinden, Regionen, in denen Tropfen eine stabile stationäre Größe besitzen, und Regionen, in denen eine Forminstabilität zu komplexer Tropfen-Dynamik führt. In der letzten Region deformieren sich Tropfen typischenweise prolat, verformen sich zu einer Hantel, und teilen sich in zwei Tochtertropfen, die wieder anwachsen. Dies kann zu Zyklen von Wachstum und Teilung von Tropfen führen, bis die Tropfen das gesamte Volumen füllen. Während spherische Tropfen durch die chemischen Reaktionen entgegen ihrer Oberflächenspannung deformiert werden, können Tropfen- Zylinder und Platten durch chemische Reaktionen stabilisiert werden. Generell ist die Dynamik von Tropfen ein hydrodynamisches Problem, da die Oberflächenspannung von deformierten Tropfen hydrodynamische Flüsse erzeugt. Wir finden, dass chemische Reaktionen entgegen die Oberflächenspannung Arbeit verrichten können, so dass die Tropfenteilung auch unter Berücksichtigung hydrodynamischer Flüsse möglich ist. Diese Doktorarbeit zeigt, dass die Kombination von chemische Reaktionen und Phasenseparation unter Nichtgleichgewichtsbedingungen zu neuem dynamischen Verhalten führen kann. Die Ergebnisse zeigen die Relevanz von chemischen Reaktionen zum Verständnis von Phasenseparation in biologischen Systemen auf, und können bei der Umsetzung der diskutierten Phänomene in experimentellen Systemen helfen. Die Tropfenteilung, die in dieser Doktorarbeit diskutiert wird, erinnert an die Teilung von biologischen Zellen. Davon motiviert schlagen wir vor, dass die Teilung von chemisch aktiven Tropfen ein Mechanismus für die Replikation von Tropfen-artigen Protozellen am Ursprung des Lebens gewesen sein könnte.:1. Introduction 2. Theory of multi-component phase-separating systems with chemical reactions 3. Minimal model for chemically active droplets in two formulations 4. Shape instability of spherical droplets with chemical reactions 5. Dynamical behavior of chemically active droplets 6. Shape instability of droplets with various geometries 7. Role of hydrodynamic flows in chemically driven droplet division 8. Chemically active droplets as a model for protocells at the origin of life 9. Conclusion AppendicesIn our everyday environment, we regularly encounter liquid-liquid phase separation in physical systems such as oil droplets in vinegar. These droplets tend to be chemically inert. In biological cells, protein and RNA may together form liquid droplets. Cells are chemically active, so that droplet components can be created, degraded and modified. In this thesis we study the influence of nonequilibrium chemical reactions on the shape dynamics of a droplet theoretically, using analytical and numerical methods. To discuss the dynamical behavior that results from combining phase separation and chemical reactions in sustained nonequilibrium conditions, we introduce a minimal model with only two components that separate into distinct phases. These two components are converted into each other by chemical reactions. The reactions are kept out of equilibrium by breaking of detailed balance, so that the droplet becomes active. We concentrate on the case where the reaction inside the droplet degrades droplet material into the outer component, and where the reaction outside creates new droplet material. We find that chemically active droplets have a rich dynamic phase space, with regions where droplets shrink and vanish, regions where droplets have a stable stationary size, and regions where the flux-driven instability leads to complex dynamic behavior of droplets. In the latter, droplets typically elongate into a dumbbell shape and then split into two symmetrical daughter droplets. These droplets then grow until they have the same size as the initial droplet. This can lead to cycles of growth and division, so that an initial droplet divides until droplets fill the simulation volume. We analyze the stationary spherical state of the droplet, which is created by a balance of the fluxes driven by the chemical reactions. We find that stationary droplets may have a shape instability, which is driven by the continuous fluxes across the droplet interface and which may trigger the division. We also find that while reactions may destabilize spherical droplet shapes despite the surface tension of the droplet, they can have stabilizing effects on cylindrical droplets and droplet plates. Generally, the shape dynamics of droplets is a hydrodynamic problem because surface tension in non-spherical droplets drives hydrodynamic flows that redistribute material and deform the droplet shape. We therefore study the influence of hydrodynamic flows on the shape changes of chemically active droplets. We find that chemical reactions in active droplets can perform work against surface tension and flows, so that the droplet division is possible even in the presence of hydrodynamic flows. The present thesis highlights how the combination of basic physical behaviors – phase separation and chemical reactions – may create novel dynamic behavior under sustained nonequilibrium conditions. The results demonstrate the importance of considering chemical reactions for understanding the dynamics of droplets in biological systems, as well as proposes a minimalist model for experimentalists that are interested in creating a system of dividing droplets. Finally, the division of chemically active droplets is reminiscent of the division of biological cells, and it motivates us to propose that chemically active droplets could have provided a simple mechanism for the self-replication of droplet-like protocells at the origin of life.:1. Introduction 2. Theory of multi-component phase-separating systems with chemical reactions 3. Minimal model for chemically active droplets in two formulations 4. Shape instability of spherical droplets with chemical reactions 5. Dynamical behavior of chemically active droplets 6. Shape instability of droplets with various geometries 7. Role of hydrodynamic flows in chemically driven droplet division 8. Chemically active droplets as a model for protocells at the origin of life 9. Conclusion Appendice

Simulations of Unsteady Shocks via a Finite-Element Solver with High-Order Spatial and Temporal Accuracy

This research aims to improve the modeling of stationary and moving shock waves by adding an unsteady capability to an existing high-spatial-order, finite-element, streamline upwind/Petrov-Galerkin (SU/PG), steady-state solver and using it to examine a novel shock capturing technique. Six L-stable, first- through fourth-order time-integration methods were introduced into the solver, and the resulting unsteady code was employed on three canonical test cases for verification and validation purposes: the two-dimensional convecting inviscid isentropic vortex, the two-dimensional circular cylinder in cross ow, and the Taylor-Green vortex. Shock capturing is accomplished in the baseline solver through the application of artificial diffusion in supersonic cases. When applied to inviscid problems, especially those with blunt bodies, numerical errors from the baseline shock sensor accumulated in stagnation regions, resulting in non-physical wall heating. Modifications were made to the solver\u27s shock capturing approach that changed the calculation of the artificial diffusion flux term (Fad) and the shock sensor. The changes to Fadwere designed to vary the application of artificial diffusion directionally within the momentum equations. A novel discontinuity sensor, derived from the entropy gradient, was developed for use on inviscid cases. The new sensor activates for shocks, rapid expansions, and other ow features where the grid is insufficient to resolve the high-gradient phenomena. This modified shock capturing technique was applied to three inviscid test cases: the blunt-body bow shock of Murman, the planar Noh problem, and the Mach 3 forward-facing step of Colella and Woodward

Computational phase-field modeling

Phase-field modeling is emerging as a promising tool for the treatment of problems with interfaces. The classical description of interface problems requires the numerical solution of partial differential equations on moving domains in which the domain motions are also unknowns. The computational treatment of these problems requires moving meshes and is very difficult when the moving domains undergo topological changes. Phase-field modeling may be understood as a methodology to reformulate interface problems as equations posed on fixed domains. In some cases, the phase-field model may be shown to converge to the moving-boundary problem as a regularization parameter tends to zero, which shows the mathematical soundness of the approach. However, this is only part of the story because phase-field models do not need to have a moving-boundary problem associated and can be rigorously derived from classical thermomechanics. In this context, the distinguishing feature is that constitutive models depend on the variational derivative of the free energy. In all, phase-field models open the opportunity for the efficient treatment of outstanding problems in computational mechanics, such as, the interaction of a large number of cracks in three dimensions, cavitation, film and nucleate boiling, tumor growth or fully three-dimensional air-water flows with surface tension. In addition, phase-field models bring a new set of challenges for numerical discretization that will excite the computational mechanics community