Dispersal and growth of bacteria

Quantitative experiments with the ability to systematically probe the system under investigation are a key element to gain insight and understanding. We present a novel and simple technique enabling the maintenance and controlled perturbation of experimental conditions of microorganisms from bacteria to nematodes. Polyacrylamide-based devices...

Spatial organization in nano-sculptured bacteria, a tale of shape, scale, patterns, and genomes

One of the most basic features that pervade biology is the existence of boundaries that separate living cells from their outer environments. Molecules responsible for the internal organization of a living cell must adapt to its boundaries, as the cell grows, divides, and changes in shape and size. In this thesis, we aim to understand how...

Nano-Workbench: A Combined Hollow AFM Cantilever and Robotic Manipulator

To manipulate liquid matter at the nanometer scale, we have developed a robotic assembly equipped with a hollow atomic force microscope (AFM) cantilever that can handle femtolitre volumes of liquid. The assembly consists of four independent robots, each sugar cube sized with four degrees of freedom. All robots are placed on a single platform...

The effects of chemical interactions and culture history on the colonization of structured habitats by competing bacterial populations

Background Bacterial habitats, such as soil and the gut, are structured at the micrometer scale. Important aspects of microbial life in such spatial ecosystems are migration and colonization. Here we explore the colonization of a structured ecosystem by two neutrally labeled strains of Escherichia coli. Using time-lapse microscopy we studied the...

Growth dynamics of single bacterial cells

Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria

Background: Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this...

Dynamics of droplet breakup in a T-junction

The breakup of droplets due to creeping motion in a confined microchannel geometry is studied using three-dimensional numerical simulations. Analogously to unconfined droplets, there exist two distinct breakup phases: (i) a quasi-steady droplet deformation driven by the externally applied flow; and (ii) a surface-tension-driven three-dimensional...

Nano- and micro-fabrication for single-molecule biological studies

Heterogeneity is a general feature in biological system. In order to avoid possible misleading effects of ensemble averaging, and to ensure a correct understanding of the biological system, it is very important to look into individuals, such as a single bio-molecule or a single cell, for details. The size of a single bio-molecule/cell typically...

Robustness and accuracy of cell division in Escherichia coli in diverse cell shapes

Cell division in typical rod-shaped bacteria such as Escherichia coli shows a remarkable plasticity in being able to adapt to a variety of irregular cell shapes. Here, we investigate the roles of the Min system and the nucleoid-occlusion factor SlmA in supporting this adaptation. We study “squeezed” E. coli in narrow nanofabricated channels...

Slow growth of the Rayleigh-Plateau instability in aqueous two phase systems

This paper studies the Rayleigh-Plateau instability for co-flowing immiscible aqueous polymer solutions in a microfluidic channel. Careful vibration-free experiments with controlled actuation of the flow allowed direct measurement of the growth rate of this instability. Experiments for the well-known aqueous two phase system (ATPS, or aqueous...

Microfluidic systems for the analysis of viscoelastic fluid flow phenomena in porous media

In this study, two microfluidic devices are proposed as simplified 1-D microfluidic analogues of a porous medium. The objectives are twofold: firstly to assess the usefulness of the microchannels to mimic the porous medium in a controlled and simplified manner, and secondly to obtain a better insight about the flow characteristics of...

In situ study of hydrogen silsesquioxane dissolution rate in salty and electrochemical developers

In order to better characterize the development of the electron-beam resist hydrogen silsesquioxane (HSQ), the authors used a quartz crystal microbalance (QCM) to study its rate of dissolution in situ. The authors determined the effect of both salt concentration and applied electric potential on the development rate of HSQ. The development rates...

Optofluidic microsystem for on-chip L2-waveguide modulation featuring flow stabilization and a novel input coupling region

We present an optofluidic microsystem integrated onto a single device featuring on-chip light guiding and positioning under stable and low-loss conditions. Integration of optical components onto a microfluidic chip offers numerous new possibilities in the field of particle and cell analysis, but reconfigurable on-chip light positioning is still...

Miniaturized flow cytometer with 3D hydrodynamic particle focusing and integrated optical elements applying silicon photodiodes

In this study, the design, realization and measurement results of a novel optofluidic system capable of performing absorbance-based flow cytometric analysis is presented. This miniaturized laboratory platform, fabricated using SU-8 on a silicon substrate, comprises integrated polymer-based waveguides for light guiding and a biconcave cylindrical...

Formation and Transport of Bubbles in Microfluidic Systems

Precise manipulation of minute volumes of fluids is at the heart of microfluidics and opens up an exciting route to miniaturize processes in the areas of chemistry, biology and medicine. An attractive way to transport small fluid samples through the channels of microfluidic devices is by enclosing these samples inside containers in the form of...

Numerical simulations of rarefied gas flows in thin film processes

Many processes exist in which a thin film is deposited from the gas phase, e.g. Chemical Vapor Deposition (CVD). These processes are operated at ever decreasing reactor operating pressures and with ever decreasing wafer feature dimensions, reaching into the rarefied flow regime. As numerical simulation tools are frequently used to design and...

Development of a miniaturized total chemical analysis system for real-time monitoring of fermentations