Structural and mechanistic insights into pore formation by proteins of the membrane attack complex/perforin superfamily

Members of the membrane attack complex/perforin (MACPF) superfamily of pore-forming proteins are characterised by a common three-dimensional fold able to puncture lipid membranes. They are found in bacterial and eukaryotes, and include immune effectors, toxins and pathogenic virulence factors. Their conserved pore-forming domain follows the same mechanism whereby two bundles of α-helices unfurl into membrane-spanning β-hairpins. This thesis provides insights into the effects of MACPF proteins on biological membranes. Coarse-grain molecular dynamics simulations of the membrane attack complex (MAC) bound to its inhibitor CD59 reveal protein-lipid interactions and local changes in membrane thickness. These may serve as signals to recruit CD59 or the molecular machinery for MAC clearance. Some bacterial MACPF proteins called cholesterol-dependent cytolysins (CDCs) hijack CD59 on human cells as part of their pore formation pathway. Atomistic simulations of CD59 in a lipid bilayer show that it samples various orientations relative to the membrane, dictating whether its binding site is available for engaging MAC or CDCs, and thus for inhibiting or promoting pore formation. CDCs assemble on cholesterol-rich lipid membranes and undergo sequential conformational changes to puncture bilayers. Site-directed mutagenesis of two CDCs reveals that an amphipathic helix in the pore-forming helical bundles is responsible for tuning the lytic activity of these proteins. Understanding the molecular basis for the function of this helix will require the high-resolution structure of a CDC late prepore intermediate. The first steps towards solving this structure by cryo-electron microscopy are presented in this thesis.Open Acces

Towards visualisation of central-cell-effects in scanning-tunnelling-microscope images of subsurface dopant qubits in silicon

Atomic-scale understanding of phosphorous donor wave functions underpins the design and optimisation of silicon based quantum devices. The accuracy of large-scale theoretical methods to compute donor wave functions is dependent on descriptions of central-cell-corrections, which are empirically fitted to match experimental binding energies, or other quantities associated with the global properties of the wave function. Direct approaches to understanding such effects in donor wave functions are of great interest. Here, we apply a comprehensive atomistic theoretical framework to compute scanning tunnelling microscopy (STM) images of subsurface donor wave functions with two central-cell-correction formalisms previously employed in the literature. The comparison between central-cell models based on real-space image features and the Fourier transform profiles indicate that the central-cell effects are visible in the simulated STM images up to ten monolayers below the silicon surface. Our study motivates a future experimental investigation of the central-cell effects via STM imaging technique with potential of fine tuning theoretical models, which could play a vital role in the design of donor-based quantum systems in scalable quantum computer architectures.Comment: Nanoscale 201

A tunable, dual mode field-effect or single electron transistor

A dual mode device behaving either as a field-effect transistor or a single electron transistor (SET) has been fabricated using silicon-on-insulator metal oxide semiconductor technology. Depending on the back gate polarisation, an electron island is accumulated under the front gate of the device (SET regime), or a field-effect transistor is obtained by pinching off a bottom channel with a negative front gate voltage. The gradual transition between these two cases is observed. This dual function uses both vertical and horizontal tunable potential gradients in non-overlapped silicon-on-insulator channel

Curve classes on irreducible holomorphic symplectic varieties

We prove that the integral Hodge conjecture holds for 1-cycles on irreducible holomorphic symplectic varieties of K3 type and of Generalized Kummer type. As an application, we give a new proof of the integral Hodge conjecture for cubic fourfolds.Comment: 15 page

A hybrid metal/semiconductor electron pump for quantum metrology

Electron pumps capable of delivering a current higher than 100pA with sufficient accuracy are likely to become the direct mise en pratique of the possible new quantum definition of the ampere. Furthermore, they are essential for closing the quantum metrological triangle experiment which tests for possible corrections to the quantum relations linking e and h, the electron charge and the Planck constant, to voltage, resistance and current. We present here single-island hybrid metal/semiconductor transistor pumps which combine the simplicity and efficiency of Coulomb blockade in metals with the unsurpassed performances of silicon switches. Robust and simple pumping at 650MHz and 0.5K is demonstrated. The pumped current obtained over a voltage bias range of 1.4mV corresponds to a relative deviation of 5e-4 from the calculated value, well within the 1.5e-3 uncertainty of the measurement setup. Multi-charge pumping can be performed. The simple design fully integrated in an industrial CMOS process makes it an ideal candidate for national measurement institutes to realize and share a future quantum ampere