Physics of Microswimmers - Single Particle Motion and Collective Behavior

Locomotion and transport of microorganisms in fluids is an essential aspect of life. Search for food, orientation toward light, spreading of off-spring, and the formation of colonies are only possible due to locomotion. Swimming at the microscale occurs at low Reynolds numbers, where fluid friction and viscosity dominates over inertia. Here, evolution achieved propulsion mechanisms, which overcome and even exploit drag. Prominent propulsion mechanisms are rotating helical flagella, exploited by many bacteria, and snake-like or whip-like motion of eukaryotic flagella, utilized by sperm and algae. For artificial microswimmers, alternative concepts to convert chemical energy or heat into directed motion can be employed, which are potentially more efficient. The dynamics of microswimmers comprises many facets, which are all required to achieve locomotion. In this article, we review the physics of locomotion of biological and synthetic microswimmers, and the collective behavior of their assemblies. Starting from individual microswimmers, we describe the various propulsion mechanism of biological and synthetic systems and address the hydrodynamic aspects of swimming. This comprises synchronization and the concerted beating of flagella and cilia. In addition, the swimming behavior next to surfaces is examined. Finally, collective and cooperate phenomena of various types of isotropic and anisotropic swimmers with and without hydrodynamic interactions are discussed.Comment: 54 pages, 59 figures, review article, Reports of Progress in Physics (to appear

Analytical Modelling and Upscaling of Multicomponent Suspension-Colloidal Transport in Porous Media

Hereby I present a PhD thesis by publications. The thesis includes seven journal papers, from which five have already been published, one has been submitted for publication and is presently under review, and another one is under final preparation to be submitted. The journal publications include high-impact-factor academic journals, e.g., Chemical Engineering Journal, Water Resources Research, Journal of Hydrology, and Transport in Porous Media, which are the major academic journals in transport in porous media. Besides that, during the PhD candidature, I have published an extended abstract in the International Journal of Chemical and Molecular Engineering, and a shared conference paper at The APPEA Journal. The thesis presents new mathematical models for transport and cotransport of colloidal and nano-particles flow in porous media. The novelties in this thesis are the development of new systems of equations, able to model phenomena that differ from the classical deep bed filtration theory, as breakthrough curves that asymptotically increase until stabilising at a lower limit than the injected concentration; prediction of non-exponential retention profiles (hyper-exponential and non-monotonic retention profiles); and the development of a new uspcaled procedure able to predict the behaviour of micro-scale particle populations. The application of colloids, engineered nano-particles, and suspension, in general, has been rapidly growing in the last two decades. The demand for these particles in several industries and processes has increased the disposal of these particles in subterranean aquifers and reservoirs. Therefore, understanding and modelling of the phenomena of particles flow through porous media have gained a lot of attention recently. In order to explain, model and predict the behaviour of the colloidal suspension and nano-particles disposal into porous structures, this thesis presents mathematical models and new physical-explanation for different phenomena that occur in porous media. Firstly, the thesis explain the transport of a single particle population that shows breakthrough curves that increase asymptotically and tends to a stabilization at a value lower than the injected concentration by two-particle capture mechanisms, where one mechanism is attachment-based on Langmuir’s blocking function, and the other mechanism is straining or size-exclusion based on constant filtration function. Secondly, the thesis proposes a new mathematical model for cotransport of a binary colloidal-species that accounts for the same two capture mechanisms previously mentioned; however, these mechanisms are applied for each particle population. The thesis also presents a new exact averaging (upscaling) procedure that results in a largescale system of equations, which significantly differs from the traditional deep bed filtration model. The proposed upscaled model is based on the average concentrations of suspended and retained particles and also includes a new site-occupation kinetic equation. Sequentially, the thesis introduces a new and simple mathematical model based on mass activity law accounting separately for single and two particles capture mechanisms, able to predict hyper-exponential retention profiles. Finally, the thesis proposes an original explanation for non-monotonic retention profiles based on a mathematical model that accounts for binary colloidal populations. This mathematical model is upscaled in radial coordinates and the behaviour non-monotonic retention profiles are predicted in reservoir-scale along with formation damage prediction. All mathematical models developed in this thesis are applicable for different areas and industrial processes and they are useful for successfully close matching of several laboratory data available in the contemporaneous literature.Thesis (Ph.D.) -- University of Adelaide, Australian School of Petroleum (ASP), 202

Nonlinear Dynamics of Carbon Steel Corrosion under Gamma Radiation

Corrosion of materials is still an unresolved problem affecting a multitude of industries. One of the grand challenges facing the corrosion community is the development of high-fidelity models for corrosion in actual service environments. The difficulties arise since corrosion involves transfer of metal atoms between the solid and solution phases thus making the system non-adiabatic. Interfacial transfer of atoms increases the chance of establishing systemic feedback between chemical reactions and transport processes, which results in chemical oscillation and periodic patterns on the corroding surfaces. These oscillating behavior in electrochemical measurements and pattern formation on corroding surfaces have been reported in certain solution environments in corrosion research. However, these corrosion phenomena have been interpreted incorrectly based on linear chemical and transport dynamics. This work presents metal oxide formation in concentric wave patterns and/or in discrete solid bands during corrosion of carbon steel. It establishes that these oxide formations are a Liesegang phenomenon occurring via strongly coupled reaction-diffusion kinetics, requiring a slow transport medium. Transition metal ions easily form hydroxides which, being hygroscopic, grow in colloidal forms or a hydrogel network. Formation of this slow transport medium induces systemic feedback between FeII/FeIII redox reactions and hydrolysis and diffusion of metal cations, and also between the processes in the gel medium and metal oxidation at the surface. Metal hydrogel formation has never previously been identified as the key condition for feedback processes and oscillation to arise in corrosion. This work is the first to demonstrate unequivocally that non-uniform deposition of metal oxides during corrosion can occur via strongly coupled solution reaction and transport processes, and not simply as a result of metallurgical non-uniformity and/or localized solution environments. This study expands our understanding of corrosion by exploring the individual processes and their non-linear interactions thus providing more insights into the development of a corrosion dynamics model. In the presence of systemic feedback, the overall corrosion dynamics cannot be expressed by a linear combination of individual elementary processes involved. To develop a reliable corrosion model when strong systemic feedback can exist, it is important to identify the key elementary processes that control the overall corrosion rate and to establish the kinetics of the elementary processes as a function of solution parameters. This study is a step toward developing such a model

Tracing back the source of contamination

From the time a contaminant is detected in an observation well, the question of where and when the contaminant was introduced in the aquifer needs an answer. Many techniques have been proposed to answer this question, but virtually all of them assume that the aquifer and its dynamics are perfectly known. This work discusses a new approach for the simultaneous identification of the contaminant source location and the spatial variability of hydraulic conductivity in an aquifer which has been validated on synthetic and laboratory experiments and which is in the process of being validated on a real aquifer

Monitoring seawater intrusion into the fractured UK Chalk aquifer using measurements of self-potential (SP)

Using laboratory, numerical and field experiments this study investigated whether borehole measurements of self-potential (SP) can be used to monitor seawater intrusion into the fractured UK Chalk aquifer. The SP, a natural voltage, arises in water saturated fractured porous media due to gradients in pressure (electrokinetic (EK) potential) and concentration (exclusion-diffusion (EED) potential), both features of seawater intrusion. An electrode array was installed in a monitoring borehole c.1.7 km from the coast, in Saltdean, East Sussex, and c.1.3 km from an active abstraction borehole. Head fluctuations in the monitoring borehole were controlled by tidal processes and seasonal changes in inland head. SP monitoring over 1.5 years revealed tidal SP signals. The fluctuations (c.600 μV) were two orders of magnitude larger than those observed at an inland site in the same aquifer, near Reading in Berkshire. Numerical simulation, supported by laboratory measurements, of the coupled hydrodynamic and electrical processes in the coastal aquifer suggested that the EK potential generated by tidal processes was one order of magnitude too small to be responsible for the tidal SP fluctuations. Instead, SP was caused by the EED potential that arose due to the concentration gradient between groundwater and seawater across the saline front (i.e. the 1000 mg/l isoline) some distance from the borehole. The saline front moved through a fracture at the base of the borehole in response to tides. A vertical SP gradient (c.0.22 mV/m), only present in the coastal borehole, was also observed. Modelling suggested that the gradient was due to the close proximity of the saline front (c.4 m) below the borehole and was caused by the EED potential. In August 2013 and 2014, tides and a decline in inland head caused saline water to enter the borehole. Fluid electrical conductivity logging showed that entry was via the fracture. Prior to each occurrence of saline breakthrough, an increase in the SP of c.300 μV was observed, commencing c.7 days before saline water was detected in the borehole. Although this study focused on a monitoring borehole, SP arrays could be installed in abstraction boreholes. The results suggest that SP monitoring may be used to provide early warning of saline water breakthrough, allowing for improved management of groundwater resources in coastal aquifers.Open Acces

A study of dead-end filtration enhanced by electric and acoustic fields

This thesis describes the experimental procedure and results of an investigation into the effect of electric and acoustic fields on dead end vacuum filtration. The test suspension used was low concentration titanium dioxide. Ultrasound energy was applied tangentially and electrical energy parallel to the filter medium. Varying electric field gradients were applied to the filter cell, either alone or together with the constant frequency acoustic field. The filter cell was based on a Nutsche filter, and allowed samples of cake to be taken at the end of the filtration experiment. Electric and acoustic field strengths, suspension characteristics and process parameters could all be varied independently. [Continues.

Self-assembled 3d photonic crystals for applications in optical communications

Nanotechnology has arisen as one of the most important fields in recent scientific research.\nIn this thesis work, the activity is mainly focused on the synthesis of nanocomposites for the fabrication of three-dimensional photonic crystals. The 3D inverse opal structures are considered very promising for their peculiar periodic properties in the confinement and propagation of light.\nTo obtain such structures, an innovative method of co-assembly has been tested, based on the self-assembly of polystyrene microspheres, in a suspension containing the infiltrating material, through a mechanism of evaporation.\nThe introduction of rare-earth ions in this ordered lattice has the purpose of studying a possible increase in light emission efficiency, due to the effect of the photonic band gap. \nIn the present study, the enhancement of the erbium emission at 1.54 microns assumes considerable importance, for future applications in optoelectronics (laser in the IR) and optical communications

Controlling and reshaping biological reaction-diffusion

Pattern formation by reaction-diffusion mechanisms is of crucial importance for the development and sustenance of all living beings. However, biological model systems so far lack the tools and versatility of the established chemical models. In this thesis, we set out to develop and expand the Min system of Escherichia coli towards becoming a universal model for biological reaction-diffusion in an in vitro setting. To this end, we firstly developed a strategy to control the Min reaction in situ. This was facilitated by incorporating a chemically synthesized azobenzene-moiety into a peptide derived from MinE. This MinE-peptide is capable of stimulating hydrolysis of ATP by MinD. Photoswitching the azobenzene crosslinker allows to also switch alpha-helicity of the peptide and therefore its activity. By periodically activating this peptide photoswitch we found resonance phenomena in the Min reaction. The photoswitch described here could thus be used in many synthetic biology scenarios, but also to learn about Min and biological reaction-diffusion systems. Secondly, we discovered that the Min system can form stationary patterns, which greatly expands the pattern diversity and therefore the phenomena which the Min model can help us understand. Especially when it comes to important decisions in development, such as cell fate or macroscopically visible effects such as fur patterns, stationary patterns are much more prominent than oscillations and waves. The discovery of these patterns also creates many opportunities for applications, especially when combined with the newly found ability of Min proteins to position arbitrary membrane-bound factors. Thirdly, this thesis shows that the Min system's complexity can be reduced even more by substituting MinE with small peptides. A combined theory-experiment approach outlines how pattern forming capabilities are restored in a small MinE-derived peptide either by adding membrane binding or by dimerizing it. This study further highlights how peptides and proteins excel as model morphogens due to their modularity and mutability. Lastly, protocols and resources are more easily available due to a combined method-paper and video that was published in open access. In conclusion, by adding tools and versatility, this thesis introduces great progress towards establishing the in vitro Min system as the ideal model for biological reaction-diffusion

Laser-Based Nano Fabrication and Nano Lithography

The improvement of fabrication resolutions is an eternal challenge for miniaturizing and enhancing the integration degrees of devices. Laser processing is one of the most widely used techniques in manufacturing due to its high flexibility, high speed, and environmental friendliness. The fabrication resolution of laser processing is, however, limited by the diffraction limit. Recently, much effort has been made to overcome the diffraction limit in nano fabrication. Specifically, combinations of multiphoton absorption by ultrafast lasers and the threshold effect associated with a Gaussian beam profile provide fabrication resolutions far beyond the diffraction limit. The use of the optical near-field achieves nano ablation with feature sizes below 100 nm. Multiple pulse irradiation from the linearly polarized ultrafast laser produces periodic nanostructures with a spatial period much smaller than the wavelength. Unlimited diffraction resolutions can also be achieved with shaped laser beams. In the meanwhile, lasers are also widely used for the synthesis of nano materials including fullerenes and nano particles. In view of the rapid advancement of this field in recent years, this Special Issue aims to introduce the state-of-the-art in nano fabrication and nano lithography, based on laser technologies, by leading groups in the field