Study of lipid bilayer behaviour modified by substrate interactions

Biological membranes rarely exist as free-floating structures but are often confined and supported by various cellular assemblies such as the cytoskeleton and the extracellular matrix. It has already been shown that biological and polymeric substrates can modulate the morphology and response to various stimuli of supported lipid bilayers significantly. The interaction between such structures and the membrane are obviously important yet remain poorly understood even in minimal or synthetic systems. The work of this thesis utilises a variety of fluorescence microscopy and atomic force microscopy (AFM) techniques to investigate the behaviour and structure of supported lipid bilayers, in particular how interfacial features of their support substrate influence and modulate their morphology and biophysical properties. First, surface modification of polydimethylsiloxane is systematically explored, in particular how the interfacial properties of such a polymer substrate can be modified to create fully and partially plasma-treated interfaces that stably support lipid bilayers. Lipid patch formation on such substrates is then investigated, revealing that the membrane undergoes significant morphological reorganisation after vesicle fusion has completed forming a lipid patch. The underlying mechanisms can be altered by substrate interactions following different pathways for fully and partially plasma-treated PDMS substrates. Furthermore, partially plasma-treated substrates are demonstrated to be capable of specifically depleting cholesterol from supported lipid membranes, while stably supporting the other remaining phospholipid species. Studies of cholesterol depletion of lipid patches possessing liquid-ordered and disordered domains reveal a disruption in domains structure, with the partitioning of fluorescent dyes into regions from which they were previously excluded. This structure perturbation was found to be reversible upon the reinsertion of cholesterol into the bilayer. Many of the discussed mechanisms are only observed in the presence of a substrate, emphasising the importance of substrate interactions in both functional biomembranes and the development of supported membrane technologie

Alpha Entanglement Codes: Practical Erasure Codes to Archive Data in Unreliable Environments

Data centres that use consumer-grade disks drives and distributed peer-to-peer systems are unreliable environments to archive data without enough redundancy. Most redundancy schemes are not completely effective for providing high availability, durability and integrity in the long-term. We propose alpha entanglement codes, a mechanism that creates a virtual layer of highly interconnected storage devices to propagate redundant information across a large scale storage system. Our motivation is to design flexible and practical erasure codes with high fault-tolerance to improve data durability and availability even in catastrophic scenarios. By flexible and practical, we mean code settings that can be adapted to future requirements and practical implementations with reasonable trade-offs between security, resource usage and performance. The codes have three parameters. Alpha increases storage overhead linearly but increases the possible paths to recover data exponentially. Two other parameters increase fault-tolerance even further without the need of additional storage. As a result, an entangled storage system can provide high availability, durability and offer additional integrity: it is more difficult to modify data undetectably. We evaluate how several redundancy schemes perform in unreliable environments and show that alpha entanglement codes are flexible and practical codes. Remarkably, they excel at code locality, hence, they reduce repair costs and become less dependent on storage locations with poor availability. Our solution outperforms Reed-Solomon codes in many disaster recovery scenarios.Comment: The publication has 12 pages and 13 figures. This work was partially supported by Swiss National Science Foundation SNSF Doc.Mobility 162014, 2018 48th Annual IEEE/IFIP International Conference on Dependable Systems and Networks (DSN

Toward Scalable Benchmarks for Mass Storage Systems

This paper presents guidelines for the design of a mass storage system benchmark suite, along with preliminary suggestions for programs to be included. The benchmarks will measure both peak and sustained performance of the system as well as predicting both short- and long-term behavior. These benchmarks should be both portable and scalable so they may be used on storage systems from tens of gigabytes to petabytes or more. By developing a standard set of benchmarks that reflect real user workload, we hope to encourage system designers and users to publish performance figures that can be compared with those of other systems. This will allow users to choose the system that best meets their needs and give designers a tool with which they can measure the performance effects of improvements to their systems