Observing magnetic objects in fluids

Observation of the motion of particles in fluids give valuable information about the particles, the environment and the interaction between them. Two distinct particle-fluid systems were studied in this framework. The first system considers centimetre-sized magnetic particles suspended in an upward water flow to create neutral buoyancy as well as a source of turbulence. This macroscopic reactor acts as an analogue simulator for microscopic self-assembly processes. From observation of the trajectories of single and two-particle systems we found that in terms of velocity, diffusion and particle interaction the laws of thermodynamics describe the macroscopic system with surprising accuracy. We have shown that we can control the amount of disturbing energy by changing the asymmetry of the water inflow, but that this method affects the particle behaviour differently in separate spatial dimensions. We found that the method used to generate disturbing energy is not that critical; also when the particles are mechanically shaken on a table in 2D, rather than in a turbulent flow in 3D, the velocity and diffusion still obey the laws of thermodynamics. The macroscopic reactor was used to study self-assembly of 3D-printed objects with embedded magnets. A system of four spheres was analysed by both humans and neural networks. Although yielding very similar results, they significantly deviate from theoretical predictions, likely due to underestimation of the disturbing energy. When using objects with anisotropic shape, we found that the geometry and aspect ratio highly define the nature of resulting structures. The particle shape for instance controls the dimensionality (1D, 2D, 3D) and flexibility (straight versus flexible angles) of the resulting assemblies. The second system involves the study of the motion of magnetotactic bacteria (MTB) under influence of varying magnetic fields. From microscopy observations of the trajectories of individual MTB we found that their response to magnetic fields accurately follows a simple model based on the ratio between magnetic and drag torque. We characterised the properties of MTB and interaction with the environment. An optical density based method was developed to monitor the properties of entire colonies of MTB with high temporal resolution. We were able to monitor four distinct parameters corresponding to growth and magnetic growth of MTB and found that these types of growth are decoupled. Although magnetic objects studied in this thesis are seemingly very distinct, with various sizes and shapes, their analysis has strong similarity. The most important aspects for fluid-particle interaction are the interplay between magnetic torque and the drag force as well as the interplay between magnetic potential energy and (equivalent) thermal energy. The parameters underpinning the models based on these concepts can be determined through observation of the motion of the particles.Beobachtung der Bewegung von Partikeln in Flüssigkeiten bringt wertvolle Informationen über die Partikel, die Umgebung als auch die Interaktion von beidem. Zwei verschiedene Partikel-Flüssigkeitssysteme wurden in dieser Studie näher untersucht. Das erste System setzte sich zusammen aus zentimeter-großen magnetischen Partikeln, ausgebracht in einem aufwärtsgerichteten Wasserstrom, welcher einen neutralen statischen Auftrieb erzeugte als auch den Ursprung von Turbulenzen darstellt. Dieser makroskopische Reaktor wurde betrieben als analoge Simulation für mikroskopische Selbstassemblierungsprozesse. Durch das Beobachten der Trajektorien von Ein- sowie Zwei-Partikelsystemen wurde festgestellt, dass die Gesetze der Thermodynamik überraschend genau das System charakterisieren, vor allem in Bezug auf Geschwindigkeit, Diffusion und Partikel-Interaktion. Wir konnten zeigen, dass wir die Stärke der Störenergie kontrollieren können durch Änderung der Asymmetrie des Wassereinlasses, aber auch das diese Methode die Partikel unterschiedlich beeinflusst, je Lage im dreidimensionalen Raum. Es konnte nachgewiesen werden, dass die Methode zur Erzeugung der Störenergie kein kritischer Einflussfaktor ist, da auch beim mechanischen Schütteln von Partikeln auf einem Tisch in 2D, im Gegensatz zu einer turbulenten Flussrate in 3D, Geschwindigkeit und Diffusion weiterhin den Gesetzen der Thermodynamik unterliegen. Der makroskopische Reaktor wurde zur Untersuchung von Selbstassemblierungsprozessen von 3D-gedruckten Objekten mit eingeschlossenen Magneten verwendet. Ein System aus vier Kugeln wurde sowohl durch Probanden als auch durch Neurale Computernetzwerk analysiert. Trotz der sehr ähnlichen Ergebnisse konnte ein signifikanter Unterschied zu den theoretischen Vorhersagen festgestellt werden, welcher höchstwahrscheinlich in der Unterschätzung der Störenergie begründet war. Bei der Benutzung von Objekten mit anisotropen Formen konnten wir zeigen, dass die Geometrie sowie das Seitenverhältnis starken Einfluss nehmen auf die entstehenden Strukturen. Die Form der Partikel hat beispielsweise entscheidenden Einfluss auf die Dimensionalität (1D, 2D, 3D) und Flexibilität (Grade vs. Flexible Winkel) der entstehenden Verbindun- gen. Das zweite System umfasste die Analyse der Bewegung von magnetotaktischen Bakterien (MTB) unter Einfluss von wechselnden Magnetfeldern. Durch mikroskopische Beobachtung der Bewegungsbahnen von einzelnen MTB konnten wir nachweisen, dass deren Bewegungsantwort auf magnetische Felder exakt einem einfachen Modell folgen, basierend auf dem Verhältnis zwischen magnetischem Drehmoment und Dreh-Strömungswiderstandes. Hierzu wurden die Eigenschaften der MTB und deren Interaktion mit der Umgebung charakterisiert. Eine Methode, basierend auf optischer Dichte-Messung, wurde entwickelt um Eigenschaften von ganzen Kolonien von MTBs mit hoher zeitlicher Auflösung zu untersuchen. Es war uns möglich vier verschiedene Parameter bezüglich Wachstum und Wachstum der magnetischen Partikel zu überwachen um festzustellen, dass diese Typen des Wachstums sich als entkoppelt darstellen. Obwohl die in dieser Doktorarbeit verwendeten magnetischen Objekte stark unterschiedlich in Bezug auf Größe und Form waren zeigte deren Auswertung hohe Ähnlichkeiten. Der wichtigste Aspekt der Partikel-Flüssigkeitsinteraktion stellt das Zusammenspiel von magnetischem Drehmoment und des Dreh-Strö- mungswiderstandes dar, als auch das Zusammenspiel der potenziellen magnetischen Energie und der (äquivalenten) thermalen Energie. Diese Parameter der Modelle konnten durch Beobachtung der Bewegung der Partikel untermauern werden, auf welchen die Konzepte des magnetischen Moments und des Strömungswiderstandes basieren

Three-dimensional self-assembly using dipolar interaction

Interaction between dipolar forces, such as permanent magnets, generally leads to the formation of one-dimensional chains and rings. We investigated whether it was possible to let dipoles self-assemble into three-dimensional structures by encapsulating them in a shell with a specific shape. We found that the condition for self-assembly of a three-dimensional crystal is satisfied when the energies of dipoles in the parallel and antiparallel states are equal. Our experiments show that the most regular structures are formed using cylinders and cuboids and not by spheroids. This simple design rule will help the self-assembly community to realize three-dimensional crystals from objects in the micrometer range, which opens up the way toward previously unknown metamaterials.Comment: 4 page

An integrated magnet array for trapping and manipulation of magnetotactic bacteria in microfluidics

We present a novel system for localized magnetic manipulation of magnetotactic bacteria in microfluidic systems. Where other methods require small conductive tracks directly below the sample, the new system consists of an array of permanent magnets switchable by a drive current to either trap or guide bacteria. This allows for much higher magnetic fields at reduced power consumption. Both a theoretical analysis and experimental analysis are presented. The system is scalable and is suited for integration in microfluidics

Long term observation of Magnetospirillum gryphiswaldense in a microfluidic channel

We controlled and observed individual magnetotactic bacteria (Magnetospirillum gryphiswaldense) inside a 5 {\mu}m high microfluidic channel for over four hours. After a period of constant velocity, the duration of which varied between bacteria, all observed bacteria showed a gradual decrease in their velocity of about 25 nm/s$^2$. After coming to a full stop, different behaviour was observed, ranging from rotation around the centre of mass synchronous with the direction of the external magnetic field, to being completely immobile. Our results suggest that the influence of the high intensity illumination and the presence of the channel walls are important parameters to consider when performing observations of such long duration.Comment: 7 pages, 11 figure

An Investigation of the Sensing Capabilities of Magnetotactic Bacteria

We investigate the sensing capabilities of magnetotactic bacteria (Magnetospirillum gryphiswaldense strain MSR1) to MCF-7 breast cancer cells. Cancer cells are allowed to grow inside a capillary tube with depth of 200 μ m and motion of magnetotactic bacteria is investigated under the influence of oxygen gradient and geomagnetic field. The influence of cancer cells is modeled to predict the oxygen gradient within the capillary tube in three-dimensional space. Our experimental motion analysis and count of motile magnetotactic bacteria indicate that they migrate towards less-oxygenated regions within the vicinity of cancer cells. Bands of magnetotactic bacteria with average concentration of 18.8±2.0% are observed in close proximity to MCF-7 cells (h = 20~ μ m), whereas the concentration at proximity of 190~ μ m is 5.0 ± 6.8%

Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts

Metastasizing tumor cells show increased expression of the intermediate filament (IF) protein vimentin, which has been used to diagnose invasive tumors for decades. Recent observations indicate that vimentin is not only a passive marker for carcinoma, but may also induce tumor cell invasion. To clarify how vimentin IFs control cell adhesions and migration, we analyzed the nanoscale (30–50 nm) spatial organization of vimentin IFs and cell-matrix adhesions in metastatic fibroblast cells, using three-color stimulated emission depletion (STED) microscopy. We also studied whether wild-type and phospho-deficient or -mimicking mutants of vimentin changed the size and lifetime of focal adhesions (FAs), cell shape, and cell migration, using live-cell total internal reflection imaging and confocal microscopy. We observed that vimentin exists in fragments of different lengths. Short fragments were mostly the size of a unit-length filament and were mainly localized close to small cell-matrix adhesions. Long vimentin filaments were found in the proximity of large FAs. Vimentin expression in these cells caused a reduction in FAs size and an elongated cell shape, but did not affect FA lifetime, or the speed or directionality of cell migration. Expression of a phospho-mimicking mutant (S71D) of vimentin increased the speed of cell migration. Taken together, our results suggest that in highly migratory, transformed mesenchymal cells, vimentin levels control the cell shape and FA size, but not cell migration, which instead is linked to the phosphorylation status of S71 vimentin. These observations are consistent with the possibility that not only levels, but also the assembly status of vimentin control cell migration

Performance and application of an open source automated magnetic optical density meter for analyzing magnetotactic bacteria

We present a spectrophotometer (optical density meter) combined with electromagnets dedicated to the analysis of magnetotactic bacteria. We have ensured that our system, called MagOD, can be easily reproduced by providing the source of the 3D prints for the housing, electronic designs, circuit board layouts, and microcontroller software. We compare the performance of this novel system to existing adapted commercial spectrophotometers. In addition, we demonstrate its use by analyzing the absorbance of magnetotactic bacteria as a function of their orientation with respect to the light path and their speed of reorientation after the field has been rotated by 90o. We continuously monitored the development of a culture of magnetotactic bacteria over a period of five days, and measured the development of their velocity distribution over a period of one hour. Even though this dedicated spectrophotometer is relatively simple to construct and cost-effective, a range of magnetic field-dependent parameters can be extracted from suspensions of magnetotactic bacteria. Therefore, this instrument will help the magnetotactic research community to understand and apply this intriguing micro-organism

An open-source automated magnetic optical density meter for analysis of suspensions of magnetic cells and particles

We present a spectrophotometer (optical density meter) combined with electromagnets dedicated to the analysis of suspensions of magnetotactic bacteria. The instrument can also be applied to suspensions of other magnetic cells and magnetic particles. We have ensured that our system, called MagOD, can be easily reproduced by providing the source of the 3D prints for the housing, electronic designs, circuit board layouts, and microcontroller software. We compare the performance of our system to existing adapted commercial spectrophotometers. In addition, we demonstrate its use by analyzing the absorbance of magnetotactic bacteria as a function of their orientation with respect to the light path and their speed of reorientation after the field has been rotated by 90°. We continuously monitored the development of a culture of magnetotactic bacteria over a period of 5 days and measured the development of their velocity distribution over a period of one hour. Even though this dedicated spectrophotometer is relatively simple to construct and cost-effective, a range of magnetic field-dependent parameters can be extracted from suspensions of magnetotactic bacteria. Therefore, this instrument will help the magnetotactic research community to understand and apply this intriguing micro-organism