Fundamental Applications of Nanopores: Controlled DNA Translocations to Nanofluidics

Nanopores are nanometer sized openings that are the connection between two electrolyte filled reservoirs. The measurement of the ion transport flowing through such a pore allows to probe physically or biologically interesting phenomena. These range from the passage of biological molecules, to the modulation of current due to multiple physical effects when the nanopore undergoes mechanical strain or pressure induced flow. Many types of nanopores exist: biological protein pores engineered to be able to sequence DNA, glass nanocapillaries easily interfaced with optical tools, or silicon nitride membrane pores which are a standard tool of recent nanotechnology.

This thesis is split into two parts. The first focuses on the use of glass nanocapillaries which allow the facile combination of nanopore experiments with optical tweezers. Optical tweezers are a well established single molecule tool that allow precise force measurement on biologically relevant scales. They are used here for the control of DNA passing through the nanopore. Their ability to measure small scale forces allows the detailed investigation of DNA binding proteins, and attempts to measure the force of DNA passage through biological pores. Extensions of these experiments to the elastic behaviour of DNA during its passage through a nanopore reveal the effects of flow generated by the charged surface of nanopores themselves. This motivates attempts to control such flows as well as the second part of the thesis.

The second part of the thesis focuses on nanofluidics, the role of fluid flow and ion transport at the nanoscale. Using a setup combining pressure with nanopores it is possible to probe, via precise measurements of the conduction of the nanopore, the wetting state of the pore. Contamination phenomena are shown to be abundant with such small systems and a description of their effects on standard measurements such as direct current current-voltage curves is given. Following this, pressure is applied to perfectly filled pores and, thanks to a new alternating current detection method, is shown to be able to discern the effect of pressure induced strain at the pore as well as the coupling of hydraulic flow with electrical properties of the pore. Finally, extensions beyond aqueous solvents are explored in both nanocapillaries and silicon nitride pores. For this, room-temperature ionic liquids are used. These liquids are known from previous studies to behave differently at surfaces and in nano-confinement. The nanopore system both with and without added pressure is shown to be a good tool for investigating such phenomena.

Quantum optomechanics at room temperature

Hendrik Schütz

Why are classical theories often sufficient to describe the physics of our world even though everything around us is entirely composed of microscopic quantum systems? The boundary between these two fundamentally dissimilar theories remains an unsolved problem in modern physics. Position measurements of small objects allow us to probe the area where the classical approximation breaks down. In quantum mechanics, Heisenbergâs uncertainty principle dictates that any measurement of the position must be accompanied by measurement induced back-action---in this case manifested as an uncertainty in the momentum. In recent years, cavity optomechanics has become a powerful tool to perform precise position measurements and investigate their fundamental limitations. The utilization of optical micro-cavities greatly enhances the interaction between light and state-of-the-art nanomechanical oscillators. Therefore, quantum mechanical phenomena have been successfully observed in systems far beyond the microscopic world. In such a cavity optomechanical system, the fluctuations in the position of the oscillator are transduced onto the phase of the light, while fluctuations in the amplitude of the light disturb the momentum of the oscillator during the measurement. As a consequence, correlations are established between the amplitude and phase quadrature of the probe light. However, so far, observation of quantum effects has been limited exclusively to cryogenic experiments, and access to the quantum regime at room temperature has remained an elusive goal because the overwhelming amount of thermal motion masks the weak quantum effects. This thesis describes the engineering of a high-performance cavity optomechanical device and presents experimental results showing, for the first time, the broadband effects of quantum back-action at room temperature. The device strongly couples mechanical and optical modes of exceptionally high quality factors to provide a measurement sensitivity

\sim\!10^4

times below the requirement to resolve the zero-point fluctuations of the mechanical oscillator. The quantum back-action is then observed through the correlations created between the probe light and the motion of the nanomechanical oscillator. A so-called âvariational measurementâ, which detects the transmitted light in a homodyne detector tuned close to the amplitude quadrature, resolves the quantum noise due to these correlations at the level of 10% of the thermal noise over more than an octave of Fourier frequencies around mechanical resonance. Moreover, building on this result, an additional experiment demonstrates the ability to achieve quantum enhanced metrology. In this case, the generated quantum correlations are used to cancel quantum noise in the measurement record, which then leads to an improved relative signal-to-noise ratio in measurements of an external force. In conclusion, the successful observation of broadband quantum behavior on a macroscopic object at room temperature is an important milestone in the field of cavity optomechanics. Specifically, this result heralds the rise of optomechanical systems as a platform for quantum physics at room temperature and shows promise for generation of ponderomotive squeezing in room-temperature interferometers.

EPFL2017

Biosystem for the culture and electrical characterisation of epithelial cell tissues

Serge Hediger

The aim of this work was to develop a microchamber system for performing electrophysiological measurements on epithelial surface on culture membranes in the mm2 range. This miniaturised system permits the use of small quantities of epithelial cells, which in relatively short time grow into a tight layer that can be used in electrophysiological (ion transport) experiments. Availability of cells is an issue, for example when the cells originate from human biopsies or from (expensive!) transgenic mice. Apart from having reduced culture surfaces (for use with scarce biological tissues), there are tremendous advantages in having a cell culture mini-chamber. Our systems are with integrated electrical electrodes, micro-fluidic channels and feed-throughs, making them extremely compact and easy to use, thereby avoiding cell perturbation by manipulations. The structures facilitate control of the cell layer growth, the measurement of the cell layer resistance and the transport and diffusion of biological or pharmacological molecules through the cell layer. Moreover we have chosen cheap and easy-to-tool materials for the realisation of disposable devices. We have also fabricated modular devices, in which the cell culture membranes can be reversibly placed within or removed from the system, thereby offering flexibility and economic interest. These microsystems (for biological applications ("biosystems")) are realised using photolithography, various etching procedures (among which powder-blasting), thin film deposition, electrochemical deposition, polydimethylsiloxane (PDMS) moulding and gluing technologies. Both electrical and fluidic characterisation of the biosystems has been performed. Also, a specific study of microelectrode properties of different electrode materials, such as Pt, Ag and Ag/AgCl has been done using various electrochemical experiments and models. The devices are finally tested in real biological experiments. These experiments were carried on with the collaboration of three different biological academic work groups: the group of Prof. W. Hunziker from the Institute of Biochemistry at the University of Lausanne, the group of Prof. Van der Goot from the Department of Biochemistry at the University of Geneva and Prof. J.D. Horisberger from the Institute of Pharmacology and Toxicology at the University of Lausanne. The functionality of our devices has been tested and their potential for the study of transport and diffusion of biological or pharmacological molecules through the cell layer via accurate measurement of (bio-) chemically induced resistance variations, has been demonstrated.

EPFL2002

Electron Cloud and Synchrotron Radiation characterization of technical surfaces with the Large Hadron Collider Vacuum Pilot Sector

Elena Buratin

This PhD thesis presents the experimental study on electron cloud (EC) and synchrotron radiation (SR) phenomena affecting the LHC storage ring performance. These phenomena are one of the major issues of the LHC storage ring, generating beam instabilities, pressure rise and heat loads on the beam pipes. This experimental study is carried out with an innovative system installed in a room temperature and field free section of the Large Hadron Collider (LHC), the Vacuum Pilot Sector (VPS). ln this system, several surfaces are simultaneously tested, in particular standard copper, amorphous carbon coating, NEG. Thanks to a wide spectrum of detectors, the EC and SR signals were studied as a function of beam parameters and beam pipe properties. The EC behaviour increases linearly with the number of bunches and bunch population above the multipacting threshold. This phenomenon increases linearly also with the bunch length for the Long Straight Sections of LHC (LSS). As expected, the bunch spacing has a crucial importance on the formation of EC dynamic: the 50 ns filling scheme avoids the multipacting effect at 450 GeV. At 6.5 TeV the photoelectron contribution is visible, with no multipacting. This scheme is not sufficient for the LHC collision studies and cannot be used as standard filling scheme. Instead, the 25 ns bunch spacing scheme suffers of EC; in this case this phenomenon can be drastically reduced only by bombarding the surface with electrons during dedicated scrubbing runs, or thanks to the installation of beam pipe surface with a low SEY, such as the amorphous-carbon coating. The measurements performed with pick-ups show the evolution of the EC dynamics for the first time in the LHC. The energy spectrum detectors and the gas analysers were also installed for the first time in the LHC history: the electron cloud spectrum and the gas composition could be measured during the machine operation. The electron energy spectrum evidences a peak at around 100 eV, corresponding to the accelerated electrons responsible for multipacting. The gas analysers measured the main gasses present in the LHC ultra-high vacuum system, such as methane, carbon dioxide and monoxide, water, hydrogen and traces of 2-Propynenitrile 3-fluoro (C3FN), probably linked to the effect of radiation into the kapton cables. It has been possible to estimate the Electron Stimulated Desorption (ESD) parameter of a copper surface as a function of the accumulated electron dose. The heat loads due to impedance, EC and SR were measured and, finally, the operation of HL-LHC machine has been estimated in terms of electron current, pressure and power deposition thanks to the results of this study. Doubling of the bunch population will increase the electron current and the pressure of one order of magnitude, while the deposited power due to EC will be smaller than 1 W/mchamber for a beam pipe SEY lower than 1.8.

EPFL2020