Bead-Based Hydrodynamic Simulations of Rigid Magnetic Micropropellers

The field of synthetic microswimmers, micro-robots moving in aqueous environments, has evolved significantly in the last years. Micro-robots actuated and steered by external magnetic fields are of particular interest because of the biocompatibility of this energy source and the possibility of remote control, features suited for biomedical applications. While initial work has mostly focused on helical shapes, the design space under consideration has widened considerably with recent works, opening up new possibilities for optimization of propellers to meet specific requirements. Understanding the relation between shape on the one hand and targeted actuation and steerability on the other hand requires an understanding of their propulsion behavior. Here we propose hydrodynamic simulations for the characterization of rigid micropropellers of any shape, actuated by rotating external magnetic fields. The method consists of approximating the propellers by rigid clusters of spheres. We characterize the influence of model parameters on the swimming behavior to identify optimal simulation parameters using helical propellers as a test system. We then explore the behavior of randomly shaped propellers that were recently characterized experimentally. The simulations show that the orientation of the magnetic moment with respect to the propeller's internal coordinate system has a strong impact on the propulsion behavior and has to be known with a precision of ≤ 5° to predict the propeller's velocity-frequency curve. This result emphasizes the importance of the magnetic properties of the micropropellers for the design of desired functionalities for potential biomedical applications, and in particular the importance of their orientation within the propeller's structure

Brownian fluctuations and hydrodynamics of a microhelix near a solid wall

We combine two-photon lithography and optical tweezers to investigate the Brownian fluctuations and propeller characteristics of a microfabricated helix. From the analysis of mean squared displacements and time correlation functions we recover the components of the full mobility tensor. We find that Brownian motion displays correlations between angular and translational fluctuations from which we can directly measure the hydrodynamic coupling coefficient that is responsible for thrust generation. By varying the distance of the microhelices from a no-slip boundary we can systematically measure the effects of a nearby wall on the resistance matrix. Our results indicate that a rotated helix moves faster when a nearby no-slip boundary is present, providing a quantitative insight on thrust enhancement in confined geometries for both synthetic and biological microswimmers

Advances in colloidal manipulation and transport via hydrodynamic interactions

In this review article, we highlight many recent advances in the field of micromanipulation of colloidal particles using hydrodynamic interactions (HIs), namely solvent mediated long-range interactions. At the micrsocale, the hydrodynamic laws are time reversible and the flow becomes laminar, features that allow precise manipulation and control of colloidal matter. We focus on different strategies where externally operated microstructures generate local flow fields that induce the advection and motion of the surrounding components. In addition, we review cases where the induced flow gives rise to hydrodynamic bound states that may synchronize during the process, a phenomenon essential in different systems such as those that exhibit self-assembly and swarming

Focused optical beams for driving and sensing helical and biological microobjects

A novel and interesting approach to detect microfluidic dynamics at a very small scale is given by optically trapped particles that are used as optofluidic sensors for microfluidic flows. These flows are generated by artificial as well as living microobjects, which possess their own dynamics at the nanoscale. Optical forces acting on a small particle in a laser beam can evoke a three dimensional trapping of the particle. This phenomenon is called optical tweezing and is a consequence of the momentum transfer from incident photons to the confined object. An optically confined particle shows Brownian motion in an optical tweezer, but is prevented from long term diffusion. A careful analysis of the motion of the confined particle allows a precise detection of microfluidic flows generated by an artificial or living source in the close vicinity of the particle. Thus, the particle can be used as a sensitive optofluidic detector. For this aim, several optical tweezers at different wavelengths are integrated into a dark-field microscope, combined with a high speed camera, to achieve a precise detection of the motion of the center-of-mass of the trapped particle. With this unique experimental system, a gold sphere is used as an optofluidic nanosensor to analyze for the first time the microfluidic oscillations generated by a biological sample. Here, a freely swimming larva of Copepods serves as the living source of flow. However, even if the trapping laser wavelength is off-resonant to the plasmon resonance of the flow detector, a finite heating of the gold nanoparticle occurs which reduces the sensitivity of detection. To increase the sensitivity of the optofluidic detection, a non-absorbing, dielectric microparticle is introduced as the optofluidic sensor for the microflows. It enables a quantitative, two dimensional mapping of the vectorial velocity field around a microscale oscillator in an aqueous environment. This paves the way for an alternative and sensitive detection approach for the microfluidic dynamics of artificial and living objects at a very small scale. To this aim and as a first step, an optically trapped microhelix serves as a model system for the mechanical and dynamical properties of a living microorganism. An optical tweezer is implemented for initiating a light-driven rotation of the chiral microobject in an aqueous environment and the optofluidic detection of its flow field is established. The method is then adopted for the measurement of the microfluidic flow generated by a biological system with similar dynamics, in this case a bacterium. The experimental approach is used to quantify the time-dependent changes of the flow generated by the flagella bundle rotation at a single cell level. This is achieved by observing the hydrodynamic interaction between a dielectric particle and a bacterium that are both trapped next to each other in a dual beam optical tweezer. This novel experimental technique allows the extraction of quantitative information on bacterial motility without the necessity of observing the bacterium directly. These findings can be of great relevance for an understanding of the response of different strains of bacteria to environmental changes and to discriminate between different states of bacterial activity

Focused optical beams for driving and sensing helical and biological microobjects

A novel and interesting approach to detect microfluidic dynamics at a very small scale is given by optically trapped particles that are used as optofluidic sensors for microfluidic flows. These flows are generated by artificial as well as living microobjects, which possess their own dynamics at the nanoscale. Optical forces acting on a small particle in a laser beam can evoke a three dimensional trapping of the particle. This phenomenon is called optical tweezing and is a consequence of the momentum transfer from incident photons to the confined object. An optically confined particle shows Brownian motion in an optical tweezer, but is prevented from long term diffusion. A careful analysis of the motion of the confined particle allows a precise detection of microfluidic flows generated by an artificial or living source in the close vicinity of the particle. Thus, the particle can be used as a sensitive optofluidic detector. For this aim, several optical tweezers at different wavelengths are integrated into a dark-field microscope, combined with a high speed camera, to achieve a precise detection of the motion of the center-of-mass of the trapped particle. With this unique experimental system, a gold sphere is used as an optofluidic nanosensor to analyze for the first time the microfluidic oscillations generated by a biological sample. Here, a freely swimming larva of Copepods serves as the living source of flow. However, even if the trapping laser wavelength is off-resonant to the plasmon resonance of the flow detector, a finite heating of the gold nanoparticle occurs which reduces the sensitivity of detection. To increase the sensitivity of the optofluidic detection, a non-absorbing, dielectric microparticle is introduced as the optofluidic sensor for the microflows. It enables a quantitative, two dimensional mapping of the vectorial velocity field around a microscale oscillator in an aqueous environment. This paves the way for an alternative and sensitive detection approach for the microfluidic dynamics of artificial and living objects at a very small scale. To this aim and as a first step, an optically trapped microhelix serves as a model system for the mechanical and dynamical properties of a living microorganism. An optical tweezer is implemented for initiating a light-driven rotation of the chiral microobject in an aqueous environment and the optofluidic detection of its flow field is established. The method is then adopted for the measurement of the microfluidic flow generated by a biological system with similar dynamics, in this case a bacterium. The experimental approach is used to quantify the time-dependent changes of the flow generated by the flagella bundle rotation at a single cell level. This is achieved by observing the hydrodynamic interaction between a dielectric particle and a bacterium that are both trapped next to each other in a dual beam optical tweezer. This novel experimental technique allows the extraction of quantitative information on bacterial motility without the necessity of observing the bacterium directly. These findings can be of great relevance for an understanding of the response of different strains of bacteria to environmental changes and to discriminate between different states of bacterial activity

Driven soft matter at the nanoscale

[eng] This thesis will present a body of articles on the research topic of soft matter. Soft matter is a research subfield of condensed matter, where the energy required for deforming the media is comparable to that of thermal fluctuations. Tipical lengthscales of these systems are of the order of micrometer (10^(-6) m) and the nanometer (10^(-6) m). It encompasses a broad range of topics, since in soft matter fluids, life and interacting matter meet. The complexity of the coupling between different interactions in soft matter can result in complex emergent responses and in a rich variety of laws that we need to understand if we want to control matter at the micro and nanoscales. In the last years, thanks to the rise of computational power, soft matter has progresively included more and more simulation methodologies to predict experimental results and pose new challenges for understanding complex behaviours at these scales. Here, the emphasis is put on the computational modelling of driven soft matter. We will present a compendium of publications, where different simulation methodologies are exploited for explaining experiments and for setting experimental challenges to be tested. We classify the presented works in two parts, the scientific approach of which differ notorously. In the first part, experiments were available and the objective was to understand emergent responses reported in the lab. Since the outcome was alreadyknown, we used simple simulation methodologies that delved into the fundamental mechanisms that lead to the response of interest. The focus of the subjects, althought diverse, was centered around dynamics of colloidal suspensions, hence a mixture of a majoritary liquid phase with a minoritary solid phase. In the second part of the thesis, we employed simulations that rigorously solved the hydrodynamics coupled to the physics of the free energy of interest. The goal was to investigate novel experimental setups, the outcome of which was unknown due to the early stage of the subject. With the simulation results, we built theories that explained the observed phenomena, setting the basis for future experimental explorations. This last part focused on two independent topics, namely, capillary driven spontaneous in lubricant infused surfaces and electrolites in charge-patterned confined nanochannels.[spa] En esta tesis se presentarán una serie de artículos en el área de investigación de la materia blanda. La materia blanda es un subcampo de la materia condensada, en el que la energía típica de los sistemas es del orden de magnitud del de las fluctuaciones térmicas. Las escalas en las que se trabaja la materia blanda suelen ser la escala micrométrica (10^(-6) m) y la nanométrica (10^(-9) m), y en estas escalas la física de fluidos convive con la física de la vida y la de la materia interacuante. Esta mezcla de interacciones puede resultar en un alto grado de complejidad y en un sín fin de respuestas emergentes que aún quedan por entender. En estos últimos años, gracias al avanze del poder computacional, se han desarrollado en la materia blanda muchas metodologías de simulación que ahora se pueden utilizar para estudiar muchas de las preguntas que aun quedan sin respuesta en la materia blanda. En esta tesis, haremos énfasis en la modelizacion computacional en este tipo de materia. Presentaremos un compendio de publicaciones, en las que hemos utilizado diferentes métodos de simulación para explicar experimentos y para postular nuevos desafíos experimentales. La tesis se divide en dos partes donde el enfoque científico varía: En la primera parte, mas centrada en coloides y micronadadores, se utilizan modelos computacionales simples para explicar efectos emergentes en experimentos de materia blanda. En la segunda parte, centrada en dinámica de fluidos, capilaridad y electrolitos se utilizan métodos mas sofisticados para intentar predecir, esta vez sin evidencia experimental alguna, los posíbles escenarios a los que podría llevar una realización experimental. Tomada en su totalidad, esta tesis se puede entender como un enfoque práctico a la hora de escoger métodos de simulación en la micro y nanoescala

Hydrodynamic effects on active colloidal suspensions

[eng] The goal of this thesis is studying hydrodynamic effects on active colloidal suspensions. Hydrodynamic interaction is propagated through the fluid in which the colloids displace due to the flow they create during their motion. It can lead to the emergence of collective phenomena, such as the self-assembly of more complex structures. Hydrodynamic interactions are not the only present in the system, since other forces may be acting between colloids, or there can be external fields acting on them such as gravity. We present our study for two different systems: magnetic colloids and Janus particles. When applying a circular magnetic field, we can induce a rotation to a particle possessing a magnetic moment. Due to the coupling of the flow with the one created by surrounding particles and with system interfaces, a rotor will eventually self-propel. Two magnetic moments interact with each other through the magnetic dipole-dipole force, which tends to align them into arrays. We study how the balance between hydrodynamic, magnetic and gravitational forces determines the morphology of the structures magnetic colloids can form. Janus particles have two faces with different chemical properties, thus the interaction between them depends on their relative orientation. We study the morphology and order of the structures that can emerge for these particles as a function of the intensity, sign and reach of the interaction between them, as well as the type of flow they create when self-propelling. Methodologically, we have combined the use of far-field theory to draw analytical expressions that have given us qualitative insight on the results we could expect with high-performance computing simulations which have allowed us to extend our study to bigger systems.[cat] En aquesta tesi ens proposem estudiar els efectes hidrodinàmics en suspensions col·loidals actives. La interacció hidrodinàmica es propaga a través del fluid en el que es desplacen els col·loids degut al flux que ells mateixos creen durant el seu moviment, podent donar lloc a l’emergència de fenòmens col·lectius, com l’autoorganització en estructures més complexes. Les interaccions hidrodinàmiques no són les úniques presents en el sistema, ja que pot haver-hi d’altres forces actuant entre els col·loids, o podem considerar l’efecte d’altres camps com la gravetat. Presentem el nostre estudi per a dos sistemes diferents: col·loids magnètics i partícules Janus. En aplicar un camp magnètic circular, es pot induir una rotació a una partícula que posseeixi un moment magnètic. Degut a l’acoplament del flux amb el creat per altres partícules i les parets del sistema, un rotor pot acabar desplaçant-se. Dos moments magnètics interactuen entre ells mitjançant la força dipolar, que afavoreix el seu alineament i la formació de cadenes de col·loids. Estudiem com el balanç entre interaccions hidrodinàmiques, magnètiques i efectes gravitatoris afecta a la morfologia de les estructures que poden formar els col·loids magnètics. Les partícules Janus tenen dues cares amb propietats químiques diferents, quelcom que dóna lloc a una interacció entre elles que depèn de la seva orientació relativa. Estudiem les estructures que poden aparèixer per a aquestes partícules com a funció de la intensitat, signe i abast d’aquesta interacció, així com de la forma del flux que creen en desplaçar-se. Metodològicament, hem combinat expressions analítiques aproximades per tenir una idea qualitativa dels fenòmens que hom pot esperar amb simulacions per ordinador per poder estudiar els fenòmens col·lectius en sistemes de més partícules

On the Properties of Self-Thermophoretic Janus Particles: From Hot Brownian Motion to Motility Landscapes

This thesis investigates several phenomena that are associated with (self-)thermophoretic Janus particles with hemispheres made from different materials serving as a paradigm for active propul- sion on the microscale. (i) The dynamics of a single Janus sphere in the external temperature field created by an immobilized heat source is studied. I show that the particle’s angular velocity is solely determined by the temperature profile on the equator between the Janus particle’s hemispheres and their phoretic mobility contrast. (ii) The distinct polarization-density patterns observed for active-particle suspensions in activity landscapes are addressed. The results of my approximate theoretical model agree well with exact numerical and measurement data for a thermophoretic microswimmer, and can serve as a template for more complex applications. The essential physics behind the formal results is robustly captured and elucidated by a schematic two-species “run- and-tumble” model. (iii) I investigate coarse-grained models of suspended self-thermo- phoretic microswimmers. Starting from atomistic molecular dynamics simulations, the coarse-grained de- scription of the fluid in terms of a local molecular temperature field is verified, and effective nonequilibrium temperatures characterizing the particle’s so called hot Brownian motion are mea- sured from simulations. They are theoretically shown to remain relevant for any further spatial coarse-graining towards a hydrodynamic description of the entire suspension as a homogeneous complex fluid.In dieser Arbeit untersuche ich mehrere Phänomene, die im Zusammenhang mit (selbst-)thermo- phoretischen Janusteilchen auftreten. Diese Teilchen bestehen aus zwei Halbkugeln mit unter- schiedlichen Materialeigenschaften und dienen in dieser Arbeit als Musterbeispiel für aktive Fort- bewegung auf der Mikroskala. (i) Die Dynamik eines einzelnen Janusteilchens im externen Temper- aturfeld einer ortsfesten Heizquelle wird untersucht. Es wird gezeigt, dass die Winkelgeschwindigkeit des Teilchens ausschließlich durch das Temperaturprofil am Äquator zwischen den Hemisphären des Janusteilchens und dem Unterschied ihrer phoretischen Mobilitäten bestimmt wird. (ii) Ich befasse mich mit den charakteristischen Polarisations- und Dichteprofilen, die für aktive Teilchen in Aktivitätslandschaften beobachtet werden. Die Ergebnisse meines approximativen theoretis- chen Modells stimmen gut mit exakten numerischen Lösungen und Messdaten für einen ther- mophoretischen Mikroschwimmer überein und können als Vorlage für komplexere Anwendungen dienen. Die wesentliche Physik hinter den formalen Ergebnissen wird durch ein schematisches Zwei-Spezies-“Run-and-Tumble”-Modell erfasst und erklärt. (iii) Ich untersuche Coarse-Graining- Modelle von suspendierten selbst-thermophoretischen Mikroschwimmern. Ausgehend von atom- istischen molekulardynamischen Simulationen wird die grobkörnige (coarse-grained) Beschreibung des Fluids in Form eines lokalen molekularen Temperaturfeldes verifiziert. Anschließend berechne ich effektive Nichtgleichgewichtstemperaturen, die die sogenannte heiße Brownsche Bewegung der Teilchen charakterisieren, und vergleiche diese mit Simulationsdaten. Es wird gezeigt, dass diese effektiven Temperaturen für jede weitere räumliche Vergröberung hin zu einer hydrodynamischen Beschreibung der gesamten Suspension als homogenes komplexes Fluid relevant bleiben

Emergent Properties of Biomolecular Organization

The organization of molecules within a cell is central to cellular processes ranging from metabolism and damage repair to migration and replication. Uncovering the emergent properties of this biomolecular organization can improve our understanding of how organisms function and reveal ways to repurpose their components outside of the cell. This dissertation focuses on the role of organization in two widely studied systems: enzyme cascades and active cytoskeletal filaments.Part I of this dissertation studies the emergent properties of the spatial organization of enzyme cascades. Enzyme cascades consist of a series of enzymes that catalyze sequential reactions: the product of one enzyme is the substrate of a subsequent enzyme. Enzyme cascades are a fundamental component of cellular reaction pathways, and spatial organization of the cascading enzymes is often essential to their function. For example, cascading enzymes assembled into multi-enzyme complexes can protect unstable cascade intermediates from the environment by forming tunnels between active sites. We use mathematical modeling to investigate the role of spatial organization in three specific systems. First, we examine enzyme cascade reactions occurring in multi-enzyme complexes where active sites are connected by tunnels. Using stochastic simulations and theoretical results from queueing theory, we demonstrate that the fluctuations arising from the small number of molecules involved can cause non-negligible disruptions to cascade throughput. Second, we develop a set of design principles for a compartmentalized cascade reaction with an unstable intermediate and show that there exists a critical kinetics-dependent threshold at which compartments become useful. Third, we investigate enzyme cascades immobilized on a synthetic DNA origami scaffold and show that the scaffold can create a favorable microenvironment for catalysis. Part II of this dissertation focuses on the organization of active cytoskeletal filaments. Many mechanical processes of a cell, such as cell division, cell migration, and intracellular transport, are driven by the ATP-fueled motion of motor proteins (kinesin, dynein, or myosin) along cytoskeletal filaments (microtubules or actin filaments). Over the past two decades, researchers have been repurposing motor protein-driven propulsion outside of the cell to create systems where cytoskeletal filaments glide on surfaces coated with motor proteins. The study of these systems not only elucidates the mechanisms of force production within the cell, but also opens new avenues for applications ranging from molecular detection to computation. We examine how microtubules gliding on surfaces coated with kinesin motor proteins can generate collective behavior in response to mutualistic interactions between the filaments and motors, thereby maximizing the utilization of system components and production. To this end, we used a microtubule-kinesin system where motors reversibly bind to the surface. In experiments, microtubules gliding on these reversibly bound motors were unable to cross each other and at high enough densities began to align and form long, dense bundles. The kinesin motors accumulated in trails surrounding the microtubule bundles and participated in microtubule transport. In conclusion, our study of the emergent properties of the spatial organization of enzyme cascades and the mutualistic interactions within active systems of motor proteins and cytoskeletal filaments provides insight into both how these systems function within cells and how they can be repurposed outside of them