Universal entrainment mechanism governs contact times with motile cells

Contact between particles and motile cells underpins a wide variety of biological processes, from nutrient capture and ligand binding, to grazing, viral infection and cell-cell communication. The window of opportunity for these interactions is ultimately determined by the physical mechanism that enables proximity and governs the contact time. Jeanneret et al. (Nat. Comm. 7: 12518, 2016) reported recently that for the biflagellate microalga Chlamydomonas reinhardtii contact with microparticles is controlled by events in which the object is entrained by the swimmer over large distances. However, neither the universality of this interaction mechanism nor its physical origins are currently understood. Here we show that particle entrainment is indeed a generic feature for microorganisms either pushed or pulled by flagella. By combining experiments, simulations and analytical modelling we reveal that entrainment length, and therefore contact time, can be understood within the framework of Taylor dispersion as a competition between advection by the no slip surface of the cell body and microparticle diffusion. The existence of an optimal tracer size is predicted theoretically, and observed experimentally for C. reinhardtii. Spatial organisation of flagella, swimming speed, swimmer and tracer size influence entrainment features and provide different trade-offs that may be tuned to optimise microbial interactions like predation and infection.Comment: New analytical entrainment theory; includes Supplementary informations as Appendix; Supplementary movies available upon reques

A new method for assessing judgmental distributions

For a number of statistical applications subjective estimates of some distributional parameters - or even complete densities are needed. The literature agrees that it is wise behaviour to ask only for some quantiles of the distribution; from these, the desired quantities are extracted. Quite a lot of methods have been suggested up to now; the number of quantiles they need varies from three to nine or more. Still another method is proposed here. Individuals are asked the relatively simple task of presenting the seven values that divide the total probability mass into eight equal parts. From these so-called octiles four estimates for location, dispersion, skewness and `peakedness' are derived. Moreover, these four values uniquely determine one distribution within either the Pearson or the Johnson system. Consequently, there is no need for `optimal' approximating formulae.Estimation;Bayesian Statistics;Statistical Distribution;statistics

Probing dynamic interfaces in organic electronics

Organic semiconductors are emerging in solar cells, photodetectors, light-emitting diodes and field-effect transistors. The main advantages are the electrical transport properties that can be tailored by chemical design, and their mechanical flexibility. Applications are foreseen in the field of large-area organic electronics, where numerous discrete devices are required on low-cost substrates such as glass or plastic. Widespread introduction however is hampered by two main bottlenecks, which are the limited operational stability and the complex formulations needed for the large-area processing. The basic building block of organic electronics is the field-effect transistor; a microelectronic device used to manipulate the magnitude of a current with an external electrical field. Transistors have to be reliable under operation i.e. when biases are applied to the electrodes, the resulting device current should be constant. In organic transistors however, the on-current slowly decreases with time, an effect of which the origin is unknown. This so-called bias-stress-effect has puzzled the scientific community for more than two decades. In chapter 2 it was shown that the decrease of current with time is caused by a shift of the threshold voltage, i.e. the bias needed to turn the transistor on. The temperature dependence of the threshold voltage shift is determined to be independent of the semiconductor used. This observation led to the conclusion that the threshold voltage shift is due to a common physical origin, but the exact nature remained elusive. Additional measurement techniques were required to understand the cause of the threshold voltage shift. In chapter 3 scanning Kelvin probe microscopy (SKPM) was used to monitor trapped charges in transistors under applied bias. SKPM measures the local surface potential and provides microscopic insight in the electrical performance of organic transistors. It was shown that the potential profiles changed upon gate bias stress, but only in the channel region of the transistor. The reliability issues were found to be not due to an increase in the contact resistance, but due to trapping of charges in the channel area of the transistor. The question remained where the charges were trapped exactly. The threshold voltage shift could be due to trapping in the semiconductor or in the gate dielectric. In chapter 4 SKPM proved that charges can be stored at the dielectric-semiconductor interface even without a semiconductor present. By exfoliating the semiconductor after stress, and subsequent probing of the surface potential of the exposed gate dielectric, it was shown that the threshold voltage shift was indeed due to charge trapping in the dielectric and not in the semiconductor. In chapter 5 a scenario is proposed to explain the observed threshold voltage shift quantitatively. The model consists of two ingredients: (i) hole-assisted electrolytic production of protons from water in the accumulation layer and (ii) the subsequent diffusion of these protons into the SiO2 gate dielectric. The proposed model captures the most important features of the gate bias stress effect, such as the time dependence of the threshold voltage shift and the semiconductor-independent temperature dependence of the threshold voltage shift. The model can also explain the recovery of the transistor upon grounding all electrodes and predicts an anomaly in the current transients, which was experimentally verified in chapter 5. By combining the experimental and theoretical evidence as presented in this thesis, it was concluded that a layer of water at the gate dielectric together with diffusion of protons into the gate dielectric can explain the most important features of the bias stress effect. At the moment large area processing, like evaporation and spin coating, is top-down. A promising process technology for organic electronics is bottom-up self-assembly, which is the autonomous organization of components into patterns and structures without human intervention. Self-assembly has the advantage over conventional processing techniques that it can be made substrate selective and can potentially cover large areas uniformly. Self-assembled monolayers (SAMs) gained a great scientific and industrial interest because of their ability to change the macroscopic properties of surfaces by a single sheet of molecules. Reported surface modifications are for instance changes in workfunction, wettability and adhesion. The advances in SAM-based electronics however have been slow. To investigate the possibility of self-assembly as a processing tool to fabricate organic electronics, first a well-studied system - thiols on gold - was considered in chapter 6. Thiols with opposite built-in dipole moment were chosen and in this way the workfunction of the injecting electrode could be increased as well as decreased. The change in workfunction resulted in a modification of the current injection. In this way patterned light-emitting diodes (LEDs) were fabricated. Only a single layer of molecules determined the light emission in an organic LED. The expertise gained on self-assembly in organic electronics was used to fabricate self-assembled monolayer electronics in chapter 7. Making integrated circuits using a bottom-up approach involving self-assembling molecules was already proposed in the 1970s. The basic building block of such an integrated circuit is the self-assembled monolayer field-effect transistor (SAMFET), where the semiconductor is a monolayer spontaneously formed on the gate dielectric. In SAMFETs fabricated so far, current modulation has only been observed in sub-micrometer channels. Low field-effect carrier mobility, low yield and poor reproducibility have prohibited the realization of bottom-up integrated circuits. We were able to identify and remove these bottlenecks by studying the charge injection and transport in monolayer semiconductors. By circumventing the main roadblocks, real logic functionality was demonstrated in integrated circuits by constructing a 15-bit code generator in which hundreds of SAMFETs were addressed simultaneously. Additionally, we investigated the cause of the absence of current in long channel length transistors. The extracted device mobility in SAMFETs was found to be determined by the monolayer coverage and the channel length. The dependence on coverage and channel length were quantitatively explained numerically and analytically. At partial coverage, SAMFETs form a unique model system to study charge percolation in two dimensions. The SAMFETs were made with silicon dioxide as the gate dielectric, which could be a possible disadvantage when they are used as building blocks in flexible electronics. As a final step the self-assembly process was transferred to organic substrates in chapter 8, which yielded fully functional 4-bit code generators based on organic dielectrics

The use of a user-centric smart mobile application prototype for supporting safety and security in a city: a design science method

Cities have always been the drivers of innovation, growth and change. Cities around the world are still rapidly expanding, especially on the African and Asian continents. Cape Town is one of those cities, where urbanisation rates are high, and crime is persisting at alarmingly high levels with crime rates being among the worst in the country and the world. Additionally, the city is home to 7 of 10 worst-performing police services in the country. Combining these factors, there is a need to look at ‘smart' ways of growth which includes facilitating a safe and secure city for citizens. Although Cape Town is pursuing smart initiatives, these have failed to place communities and individuals among the key stakeholders in the smart planning process. This research focuses on further researching smart city initiatives in Cape Town, placing citizens at the centre of the development process. As Cape Town's mobile phone penetration rate is high and access to Internet is rapidly expanding, this research aims to use crowdsourcing techniques for developing a smart mobile application prototype that is focused on enhancing community engagement and facilitating increased perceived feelings of safety and security for citizens. The study uses a Design Science Research method with Cape Town citizens as the main stakeholders, to propose an artifact based on their wishes, needs and current issues faced with regards to safety and security in the city. The proposed artifact focuses on enhancing community engagement, through a chat room and user-logged incident reports, as well as a customised safe route planning functionality where users can send emergency signals to comembers with the use of GPS live location tracking. The research shows participants are willing to adopt the use of the mobile application prototype, given there is substantial community buy-in, and the functionalities in the app are easy to use and quickly accessible. The study further identifies the need for better police follow up and involvement, as the city's police system could benefit from crowd-sourced crime-data in reducing the number of crimes in neighbourhoods to make citizens feel more safe and secure