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Glucans are polysaccharides integral to many materials and biological functions. Under the umbrella of Biomime, the Swedish Center for Biomimetic Fiber Engineering, this work has aimed to improve basic understanding of the biosynthesis of such glucans. This has been achieved through direct investigation of cellulose structure, and by developing the tools to analyze glucan biosynthesis. Notably we have identified a novel chemical effector of glucan synthesis processes and developed a proteomic toolkit useful for analyzing membrane-bound glycosyltransferases, the enzyme group responsible for glucan biosynthesis. During this work, glucan synthesis has been studied using both Gluconacetobacter and Populus cell suspension cultures. Publication I. Gluconacetobacter cellulose (BC) was used as a base to create a novel and well characterized nano-material with improved mechanical properties. This novel composite of BC and hydroxyethylcellulose (HEC) had improved tensile strength compared to pure BC. Through thorough study utilizing dispersion measurements, electron microscopy, nuclear magnetic resonance and X-ray diffraction it was shown that the improved properties derived from a layer of HEC coating each fibril. Publication II. Bacterial cellulose was labeled in specific positions with 13C (C4 and C6). These samples were analyzed by CP/MAS NMR along with cellulose samples from cotton and Halocynthia sp. For each sample spectral fitting was performed and general properties of crystal allomorph composition and fibril widths were determined. Calculations were also made for water accessible surfaces of the fibrils. The results showed that water accessible C4 surface signals are reflective of the allomorph composition of the sample, along with a distorted signal that derives due to fibril imperfections. Water accessible surface signals from the C6 region are instead derived from rotamer conformations of the C6 hydroxymethyl groupsfrom glucose residues. In Publication III, a high-throughput screen was used to identify an inhibitor of Golgi-derived glycosyltransferase activity, termed chemical A. The structural basis for inhibition was determined and in vitro assays of callose synthesis were performed. The in vitro assays revealed chemical A to also be an activator of callose synthesis. To understand this activation kinetic studies were performed, showing that chemical A is a mixed type of activator, which can bind either the free enzyme or the enzyme-substrate complex. Chemical A has uses in chemical genetics for dissecting processes involving callose synthesis, such as stress response and cell-plate formation. In publication IV, we present an in-house developed platform for proteomics with a distributed processing model. This in-house system has been central to many proteomics tasks, including for those presented in publication V, and is being distributed as the Automated Proteomics Pipeline (APP). In publication V, conditions for enrichment of Detergent-Resistant Microdomains (DRM) have been optimized for Populus trichocarpa cell cultures. The proteins enriched in DRM were identified using mass spectrometry based proteomics, and a functional model for DRM was proposed. This model involves proteins specialized in stress response, including callose synthase, and cell signaling. This further strengthens the arguments for DRMs as sites of specific cellular functions and confirms they play a role in glucan synthesis.QC 20140710</p

Numerical and experimental aspect of coherent lensless imaging

This thesis is devoted to the understanding, application, and extension of coherent lensless imaging methods for microscopy purposes. Particular attention is given to the Fourier transform holography and coherent diffractive imaging methods.These two methods share several properties such as the ability for singleshot imaging and their experimental geometries, but differ greatly in their reconstruction approach. Holographic approaches use reference waves to encode phase information into the measurements which means the reconstruction quality is controlled, to a large extent, by the characteristics of the reference wave. In contrast, coherent diffractive imaging utilizes prior knowledge to iteratively recover the phase information; this has the effect that the reconstruction quality is independent of any optics or references, but relies heavily on the performance of iterative numerical algorithms. The complex nature of the phase retrieval problem raises questions regarding the existence and uniqueness of a solution which makes understanding the numerical and mathematical aspects of the problem of central importance. The main topics in this thesis include: the extension of coherent diffractive imaging to multi-wavelength diffraction data, effects related to optically thick references in Fourier transform holography and an alternative numerical approach to phase retrieval which is based on non-rigid image registration. Along the way, various topics are covered which form the foundations of these techniques, or could be useful to a practioner in the field

Phase retrieval via non-rigid image registration

Phase retrieval is the numerical procedure of recovering a complex-valued signal from knowledge about its amplitude and some additional information. Here, an indirect registration procedure, based on the large deformation diffeomorphic metric mapping (LDDMM) formalism, is investigated as a phase retrieval method for coherent diffractive imaging. The method attempts to find a deformation which transforms an initial, template image to match an unknown target image by comparing the diffraction pattern to the data. The exterior calculus framework is used to treat different types of deformations in a unified and coordinate-free way. The algorithm performance with respect to measurement noise, image topology, and particular action are explored through numerical examples

Environmental Flow Scenarios for a Regulated River System: Projecting Catchment-Wide Ecosystem Benefits and Consequences for Hydroelectric Production

To enable prioritization among measures for ecological restoration, knowing the expected benefits and consequences of implementation is imperative but rarely explicitly quantified. We developed a novel method to prioritize among environmental flow measures to rehabilitate ecosystems in the Ume River catchment in northern Sweden, a river system heavily regulated for hydropower production. Our strategy was to identify measures with minimal impact on hydropower production while providing substantial environmental benefits. Based on field surveys of remaining natural values and potential for ecological rehabilitation, we quantified the projected gain in habitat area of implementing environmental flows for target organism groups, for example, lotic fish species and riparian vegetation, along the whole river length. We quantified the consequences for hydropower production by identifying a set of hydropower operational rules reflecting the constraints added by environmental flows. We then used production optimization software to calculate changes in hydropower production and revenues. Implementing restrictions on zero-flow events by mandating minimum discharge at all run-of-river hydropower stations and allocating 1%-12% of mean annual discharge to bypassed reaches in the entire catchment would result in a 2.1% loss of annual electricity production. Adding flow to fishways would increase the loss to 3.1% per year. With implementation of more natural water-level fluctuations in run-of-river impoundments, the loss increases to 3.8%. These actions would increase the habitat for lotic species like the grayling Thymallus more than threefold and increase the area of riparian vegetation by about 66%. Our method forms a basis for ongoing implementation of nationwide environmental rehabilitation schemes

Singleshot polychromatic coherent diffractive imaging with a high-order harmonic source

© 2020 Optical Society of America. Users may use, reuse, and build upon the article, or use the article for text or data mining, so long as such uses are for non-commercial purposes and appropriate attribution is maintained. All other rights are reserved.Singleshot polychromatic coherent diffractive imaging is performed with a high-intensity high-order harmonic generation source. The coherence properties are analyzed and several reconstructions show the shot-to-shot fluctuations of the incident beam wavefront. The method is based on a multi-step approach. First, the spectrum is extracted from double-slit diffraction data. The spectrum is used as input to extract the monochromatic sample diffraction pattern, then phase retrieval is performed on the quasi-monochromatic data to obtain the sample’s exit surface wave. Reconstructions based on guided error reduction (ER) and alternating direction method of multipliers (ADMM) are compared. ADMM allows additional penalty terms to be included in the cost functional to promote sparsity within the reconstruction

Reference shape effects on Fourier transform holography

Soft-x-ray holography which utilizes an optics mask fabricated in direct contact with the sample, is a widely applied x-ray microscopy method, in particular, for investigating magnetic samples. The optics mask splits the x-ray beam into a reference wave and a wave to illuminate the sample. The reconstruction quality in such a Fourier-transform holography experiment depends primarily on the characteristics of the reference wave, typically emerging from a small, high-aspect-ratio pinhole in the mask. In this paper, we study two commonly used reference geometries and investigate how their 3D structure affects the reconstruction within an x-ray Fourier holography experiment. Insight into these effects is obtained by imaging the exit waves from reference pinholes via high-resolution coherent diffraction imaging combined with three-dimensional multislice simulations of the x-ray propagation through the reference pinhole. The results were used to simulate Fourier-transform holography experiments to determine the spatial resolution and precise location of the reconstruction plane for different reference geometries. Based on our findings, we discuss the properties of the reference pinholes with view on application in soft-x-ray holography experiments

Challenges for 10 nm MOSFET process integration, Journal of Telecommunications and Information Technology, 2007, nr 2

An overview of critical integration issues for future generation MOSFETs towards 10 nm gate length is presented. Novel materials and innovative structures are discussed. The need for high-k gate dielectrics and a metal gate electrode is discussed. Different techniques for strain-enhanced mobility are discussed. As an example, ultra thin body SOI devices with high mobility SiGe channels are demonstrated