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  • 1.
    Adjeiwaah, Mary
    Umeå University, Faculty of Medicine, Department of Radiation Sciences.
    Quality assurance for magnetic resonance imaging (MRI) in radiotherapy2017Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Magnetic resonance imaging (MRI) utilizes the magnetic properties of tissues to generate image-forming signals. MRI has exquisite soft-tissue contrast and since tumors are mainly soft-tissues, it offers improved delineation of the target volume and nearby organs at risk. The proposed Magnetic Resonance-only Radiotherapy (MR-only RT) work flow allows for the use of MRI as the sole imaging modality in the radiotherapy (RT) treatment planning of cancer. There are, however, issues with geometric distortions inherent with MR image acquisition processes. These distortions result from imperfections in the main magnetic field, nonlinear gradients, as well as field disturbances introduced by the imaged object. In this thesis, we quantified the effect of system related and patient-induced susceptibility geometric distortions on dose distributions for prostate as well as head and neck cancers. Methods to mitigate these distortions were also studied.

    In Study I, mean worst system related residual distortions of 3.19, 2.52 and 2.08 mm at bandwidths (BW) of 122, 244 and 488 Hz/pixel up to a radial distance of 25 cm from a 3T PET/MR scanner was measured with a large field of view (FoV) phantom. Subsequently, we estimated maximum shifts of 5.8, 2.9 and 1.5 mm due to patient-induced susceptibility distortions. VMAT-optimized treatment plans initially performed on distorted CT (dCT) images and recalculated on real CT datasets resulted in a dose difference of less than 0.5%.

     The magnetic susceptibility differences at tissue-metallic,-air and -bone interfaces result in local B0 magnetic field inhomogeneities. The distortion shifts caused by these field inhomogeneities can be reduced by shimming.  Study II aimed to investigate the use of shimming to improve the homogeneity of local  B0 magnetic field which will be beneficial for radiotherapy applications. A shimming simulation based on spherical harmonics modeling was developed. The spinal cord, an organ at risk is surrounded by bone and in close proximity to the lungs may have high susceptibility differences. In this region, mean pixel shifts caused by local B0 field inhomogeneities were reduced from 3.47±1.22 mm to 1.35±0.44 mm and 0.99±0.30 mm using first and second order shimming respectively. This was for a bandwidth of 122 Hz/pixel and an in-plane voxel size of 1×1 mm2.  Also examined in Study II as in Study I was the dosimetric effect of geometric distortions on 21 Head and Neck cancer treatment plans. The dose difference in D50 at the PTV between distorted CT and real CT plans was less than 1.0%.

    In conclusion, the effect of MR geometric distortions on dose plans was small. Generally, we found patient-induced susceptibility distortions were larger compared with residual system distortions at all delineated structures except the external contour. This information will be relevant when setting margins for treatment volumes and organs at risk.  

    The current practice of characterizing MR geometric distortions utilizing spatial accuracy phantoms alone may not be enough for an MR-only radiotherapy workflow. Therefore, measures to mitigate patient-induced susceptibility effects in clinical practice such as patient-specific correction algorithms are needed to complement existing distortion reduction methods such as high acquisition bandwidth and shimming.

  • 2.
    Agvik, Simon
    Umeå University, Faculty of Science and Technology, Department of Physics.
    A deformable terrain model in multi-domain dynamics using elastoplastic constraints: An adaptive approach2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Achieving realistic simulations of terrain vehicles in their work environment does not only require a careful model of the vehicle itself but the vehicle's interactions with the surroundings are equally important. For off-road ground vehicles the terrain will heavily affect the behaviour of the vehicle and thus puts great demands on the terrain model.

    The purpose of this project has been to develop and evaluate a deformable terrain model, meant to be used in real-time simulations with multi-body dynamics. The proposed approach is a modification of an existing elastoplastic model based on linear elasticity theory and a capped Drucker-Prager model, using it in an adaptive way. The original model can be seen as a system of rigid bodies connected by elastoplastic constraints, representing the terrain. This project investigates if it is possible to create dynamic bodies just when it is absolutely necessary, and store information about possible deformations in a grid.

    Two methods used for transferring information between the dynamic bodies and the grid have been evaluated; an interpolating approach and a discrete approach. The test results indicate that the interpolating approach is preferable, with better stability to an equal performance cost. However, stability problems still exist that have to be solved if the model should be useful in a commercial product.

  • 3.
    Akhtari, Mohammad Mehdi
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Accuracy of inverse treatment planning on computed tomography like images derived from magnetic resonance data2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Treatment planning for radiotherapy involves different types of imaging to delineate target volume precisely. The most suitable sources to get 3D information of the patient are the computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET)/CT modalities. CT is a modern medical imaging technique that allows three-dimensional treatment planning and conformal treatment techniques. By combining CT images with efficient dosimetry software, accurate patient positioning methods and verification and quality assurance good results can be achieved. The CT images show how the radiation interacts with the material based on each tissue has a different attenuation coefficient, so the data can be used for dose calculations in treatment planning.

    Radiation oncology is therapeutic modality, in which irradiating cancer cells as target is the main goal while always try to limit the dose to healthy tissues and organs. CT images have good potentials because they can provide high geometrical accuracy and electron density information. Having said that, however, using CT images alone for planning does not provide enough information in order to delineate the target volume accurately because the attenuation in soft tissue is fairly constant therefore the soft tissue contrast is poor. Here, (MR) imaging can be very useful since it has superior soft tissue contrast especially in conditions such as prostate cancer, brain lesions, and head and neck tumors. It should be noted that MR images cannot provide electron density information that is required for dose calculations.

    It has been hypothesized that since MRI images have certain benefits in comparison with CT images such as its superior soft tissue contrast which improves contrast resolution between different types of tissues, it would be beneficial to use MRI alone for both target delineation and treatment planning to save time and costs. This was investigated by introducing substitute computed tomography (SCT) which can be interpreted as CT equivalent information obtained by MRI images.

    We used data from five patients with intracranial tumors, and reviewed their initial dosimetric treatment plans that were based solely on CT images, that data was also used to evaluate the dosimetric accuracy of our research treatment plans. Optimization plans that are based on CT images and substitute CT (SCT) was compared with each other in the first step. On the second step the treatment plan that was based on SCT images was transferred to the CT images without any changes and comparisons between the dose calculations on both data sets were made. The delivered dose to planning target volume (PTV) and risk organs was compared.

    Gamma index results between SCT and transferred plan showed no difference in the dose distribution map in PTV. The maximum difference was in the outer contour to the skull. The average and median dose delivered to PTV was within 0.35% difference studying in all patients.

    In conclusion for patients with intracranial tumors the dosimetric accuracy of treatment plans based on SCT and MR images were very accurate, and we demonstrated that it was possible to reach the same dose volume histograms by SCT compared to CT with minimal differences, which were not significant. 

  • 4.
    Algers, Björn
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Stereo Camera Calibration Accuracy in Real-time Car Angles Estimation for Vision Driver Assistance and Autonomous Driving2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The automotive safety company Veoneer are producers of high end driver visual assistance systems, but the knowledge about the absolute accuracy of their dynamic calibration algorithms that estimate the vehicle’s orientation is limited.

    In this thesis, a novel measurement system is proposed to be used in gathering reference data of a vehicle’s orientation as it is in motion, more specifically the pitch and roll angle of the vehicle. Focus has been to estimate how the uncertainty of the measurement system is affected by errors introduced during its construction, and to evaluate its potential in being a viable tool in gathering reference data for algorithm performance evaluation.

    The system consisted of three laser distance sensors mounted on the body of the vehicle, and a range of data acquisition sequences with different perturbations were performed by driving along a stretch of road in Linköping with weights loaded in the vehicle. The reference data were compared to camera system data where the bias of the calculated angles were estimated, along with the dynamic behaviour of the camera system algorithms. The experimental results showed that the accuracy of the system exceeded 0.1 degrees for both pitch and roll, but no conclusions about the bias of the algorithms could be drawn as there were systematic errors present in the measurements.

  • 5.
    Andersson, Axel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Real-Time Feedback for Agility Training: Tracking of reflective markers using a time-of-flight camera2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 6.
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Ion recombination in liquid ionization chambers: development of an experimental method to quantify general recombination2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    An experimental method (the two-dose-rate method) for the correction of general recombination losses in liquid ionization chambers has been developed and employed in experiments with different liquids and radiation qualities. The method is based on a disassociation of initial and general recombination, since an ionized liquid is simultaneously affected by both of these processes.

    The two-dose-rate method has been compared to an existing method for general recombination correction for liquid ionization chambers, and has been found to be the most robust method presently available.

    The soundness of modelling general recombination in liquids on existing theory for gases has been evaluated, and experiments indicate that the process of general recombination is similar in a gas and a liquid. It is thus reasonable to employ theory for gases in the two-dose-rate method to achieve experimental corrections for general recombination in liquids. There are uncertainties in the disassociation of initial and general recombination in the two-dose-rate method for low applied voltages, where initial recombination has been found to cause deviating results for different liquids and radiation qualities.

    Sensitivity to ambient electric fields has been identified in the microLion liquid ionization chamber (PTW, Germany). Experimental data may thus be perturbed if measurements are conducted in the presence of ambient electric fields, and the sensitivity has been found to increase with an increase in the applied voltage. This can prove to be experimentally limiting since general recombination may be too severe for accurate corrections if the applied voltage is low.

  • 7.
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Radiation Dosimetry for CBCT – Quality Control and Applied Dosimetry2015Conference paper (Refereed)
    Abstract [en]

    The use of Cone Beam CT (CBCT) devices in health care has increased in recent years. Unfortunately, this trend has not been followed by a standardization of dose metrics for Quality Control (QC), or a necessary evolution of applied dosimetry for assessment of patient dose.

    The European Federation of Organisations in Medical Physics (EFOMP) has drafted a report on the property of QC for CBCT devices. The report contains objective, practical and unifying methodology for QC of CBCT used in oral radiology, radiotherapy, interventional radiology and guided surgery. The dose metrics discussed include the Computed Tomography Dose Index (CTDI), Kerma-Area Product (KAP) and detector incident air kerma. The report concludes that KAP-meters are preferable for QC as long as they can be mounted on the X-ray tube housing. Otherwise measurements of detector incident kerma seem to offer a practical solution for QC.

    The European Radiation Dosimetry Group (EURADOS) are preparing a literature review on patient dose from various applications of CBCT, which will in part be included in the EFOMP report. Most studies on patient dose from CBCT examinations and interventional procedures are based on thermoluminescent dosimeter (TLD) measurements in Rando phantoms. While helpful to the community, these studies yield substantial uncertainty when applied in the clinical reality of medical physicists working with justification and optimization. Applied dosimetry for CBCT needs to evolve and adopt recent theoretical advances to allow robust estimates of patient dose.

  • 8.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Granberg, Christoffer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Riklund, Katrine
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    A novel system for quality assurance of radiology equipment2018In: Eurosafe Imaging 2018, 2018Conference paper (Refereed)
  • 9.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Johansson, Erik
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    On the property of measurements with the PTW microLion chamber in continuous beam2012In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 39, no 8, p. 4775-4787Article in journal (Refereed)
    Abstract [en]

    Purpose: The performance of liquid ionization chambers, which may prove to be useful tools in the field of radiation dosimetry, is based on several chamber and liquid specific characteristics. The present work investigates the performance of the PTW microLion liquid ionization chamber with respect to recombination losses and perturbations from ambient electric fields at various dose rates in continuous beams.

    Methods: In the investigation, experiments were performed using two microLion chambers, containing isooctane (C8H18) and tetramethylsilane (Si(CH3)4) as the sensitive media, and a NACP-02 monitor chamber. An initial activity of approximately 250 GBq 18F was employed as the radiation source in the experiments. The initial dose rate in each measurement series was estimated to 1.0 Gy min-1 by Monte Carlo simulations and the measurements were carried out during the decay of the radioactive source. In the investigation of general recombination losses, employing the two-dose-rate method for continuous beams, the liquid ionization chambers were operated at polarizing voltages 25, 50, 100, 150, 200 and 300 V. Furthermore, measurements were also performed at 500 V polarizing voltage in the investigation of the sensitivity of the microLion chamber to ambient electric fields.

    Results: The measurement results from the liquid ionization chambers, corrected for general recombination losses according to the two-dose-rate method for continuous beams, had a good agreement with the signal to dose linearity from the NACP-02 monitor chamber for general collection efficiencies above 70%. The results also displayed an agreement with the theoretical collection efficiencies according to the Greening theory, except for the liquid ionization chamber containing isooctane operated at 25 V. At lower dose rates, perturbations from ambient electric fields were found in the microLion chamber measurement results. Due to the perturbations, measurement results below an estimated dose rate of 0.2 Gy min-1 were excluded from the present investigation of the general collection efficiency. The perturbations were found to be more pronounced when the chamber polarizing voltage was increased.

    Conclusions: By using the two-dose-rate method for continuous beams, comparable corrected ionization currents from experiments in low- and medium energy photon beams can be achieved. However, the valid range of general collection efficiencies has been found to vary in a comparison between experiments performed in continuous beams of 120 kVp x-ray, and the present investigation of 511 keV annihilation photons. At very high dose rates in continuous beams, there are presently no methods that can be used to correct for general recombination losses and at low dose rates the microLion chamber may be perturbed by ambient electric fields. Increasing the chamber polarizing voltage, which diminishes the general recombination effect, was found to increase the microLion chamber sensitivity to ambient electric fields. Prudence is thus advised when employing the microLion chamber in radiation dosimetry, as ambient electric fields of the strength observed in the present work may be found in many common situations. Due to uncertainties in the theoretical basis for recombination losses in liquids, further studies on the underlying theories for the initial and general recombination effect are needed if liquid ionization chambers are to become a viable option in high precision radiation dosimetry.

  • 10.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Kaiser, Franz-Joachim
    Gómez, Faustino
    Jäkel, Oliver
    Pardo-Montero, Juan
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    A comparison of different experimental methods for general recombination correction for liquid ionization chambers2012In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 57, no 21, p. 7161-7175Article in journal (Refereed)
    Abstract [en]

    Radiation dosimetry of highly modulated dose distributions requires a detector with a high spatial resolution. Liquid filled ionization chambers (LICs) have the potential to become a valuable tool for the characterization of such radiation fields. However, the effect of an increased recombination of the charge carriers, as compared to using air as the sensitive medium has to be corrected for. Due to the presence of initial recombination in LICs, the correction for general recombination losses is more complicated than for air-filled ionization chambers. In the present work, recently published experimental methods for general recombination correction for LICs are compared and investigated for both pulsed and continuous beams. The experimental methods are all based on one of two approaches, either measurements at two different dose rates (two-dose-rate methods), or measurements at three different LIC polarizing voltages (three-voltage methods). In a comparison with the two-dose-rate methods, the three-voltage methods fail to achieve accurate corrections in several instances, predominantly at low polarizing voltages and dose rates. However, for continuous beams in the range of polarizing voltages recommended by the manufacturer of the LICs used, the agreement between the different methods is generally within the experimental uncertainties. For pulsed beams, the agreement between the methods is poor. The inaccuracies found in the results from the three-voltage methods are associated with numerical difficulties in solving the resulting equation systems, which also make these methods sensitive to small variations in the experimental data. These issues are more pronounced for the case of pulsed beams. Furthermore, the results suggest that the theoretical modelling of initial recombination used in the three-voltage methods may be a contributing factor to the deviating results observed.

  • 11.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Pavlicek, William
    Patient organ dose with computed tomography - a review of present methodology and DICOM information: executive summary of the joint report of AAPM task group 246 and EFOMP2016In: ECR 2016 Book of Abstracts, 2016, Vol. 7, no 1, article id B0303Conference paper (Refereed)
    Abstract [en]

    Purpose: The justification and optimisation of medical imaging employing ionizing radiation have been intensely discussed in recent years, particularly for computed tomography (CT). A key point in this discussion is the estimation of patient dose, which commonly employs radiation output metrics developed for quality assurance and no patient specific information. Such patient dose estimates are of limited value, and more refined methods needs to be promoted and provided to the community.

    Methods and Materials: AAPM Task Group 246 was formed in 2013, and in a joint venture with EFOMP charged with summarizing present methodology and DICOM information available for estimating patient dose with computed tomography.

    Results: The Joint Report of AAPM Task Group 246 and EFOMP is a comprehensive resource for the clinical medical physicist. The possibilities of patient specific dosimetry from the Computed Tomography Dose Index (CTDIvol), to the Size-Specific Dose Estimates (SSDE) and advanced Monte Carlo methods are discussed together with available DICOM information, as well as practical examples on how patient dose estimates can be achieved. The report also summarizes important factors contributing to the uncertainty in patient dose estimates and gives examples of achievable confidence intervals.

    Conclusion: The SSDE and Monte Carlo methods can together with detailed scanner, examination and patient specific DICOM information offer refined estimates of patient dose for justification and optimisation of CT examinations. Given the present robustness of available methods AAPM Task Group 246 and EFOMP recommend that all reports of patient dose should be accompanied by estimates of the associated uncertainty.

  • 12.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Modeling ion recombination in liquid ionization chambers: Improvement and analysis of the two-dose-rate method2017In: Medical physics (Lancaster), ISSN 0094-2405, Vol. 44, no 11, p. 5977-5987Article in journal (Refereed)
    Abstract [en]

    Purpose: The use of liquid ionization chambers can provide useful information to endeavors with radiation dosimetry for highly modulated beams. Liquid ionization chambers may be particularly suitable for computed tomography applications where conventional ionization chambers do not present a high enough sensitivity for the spatial resolution required to characterize common X-ray beams. Due to the sensitivity, which leads to high charge densities, liquid ionization chambers can suffer from large recombination losses leading to degradation in signal to dose rate linearity. To solve this problem, a two-dose-rate method for general recombination correction has been proposed for liquid ionization chambers. However, the valid range of recombination losses that the method can accurately account for has been found to vary depending on radiation quality. The present work provides an in-depth analysis of the performance of the two-dose-rate method. Furthermore, the soundness of applying gas theory to liquids is investigated by using the two-dose-rate method.

    Methods: In the present work, the two-dose-rate method for general recombination correction of liquid ionization chambers used in continuous beams is studied by employing theory for gas-filled ionization chambers. An approximate relation for the general collection efficiency containing a material-specific parameter that is traceable to liquids has been derived for theoretical and experimental investigation alongside existing theory. Furthermore, the disassociation between initial and general recombination in the method is analyzed both theoretically and experimentally.

    Results: The results indicate that liquids and gases share general recombination characteristics, where the liquids investigated (isooctane and tetramethylsilane) to a large extent mimic the behavior theoretically expected in gases. Furthermore, it is shown that the disassociation between initial and general recombination in the two-dose-rate method is an approximation that depends on the relation between initial recombination and the collecting electric field strength at the dose rates used.

    Conclusions: Due to the approximation used to separate initial and general recombination the valid range of collection efficiencies for the two-dose-rate method will not only depend on the model used to describe general recombination but also on the type of liquid and radiation beam quality. As there is no robust theory for initial recombination in liquids to apply, the valid range of general collection efficiencies for the two-dose-rate method should be experimentally evaluated for each radiation dosimetry application.

  • 13.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Tölli, Heikki
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    The Use of Liquid Ionization Chambers in Radiation Dosimetry2012In: World Congress on Medical Physics and Biomedical Engineering May 26-31, 2012 Beijing, China / [ed] Mian Long, Springer, 2012Conference paper (Refereed)
    Abstract [en]

    Liquid ionization chambers (LICs) have found applications in many fields in radiation dosimetry, e.g. IMRT, hadron therapy, brachytherapy and computed tomography. The wide range of applications is made possible due to the high sensitivity of LICs, allowing them to be manufactured with small physical dimensions of the chamber body and the effective measurement volume. Furthermore, the commonly used liquids (such as isooctane) have radiation absorption characteristics similar to water, introducing only small fluence perturbation effects as compared to conventional dosimeters. The small dimension of the effective measurement volume is beneficial for the quantification of radiation beams with steep gradients, while retaining a high measurement signal with good statistical properties. However, the interpretation of measurement results is not straight-forward due to several factors influencing their performance. Here, the main problems are recombination effects and particle type- and energy dependence, which may cause severe non-linear effects. The loss of measurement signal in LICs is due to both initial and general recombination. In the present work it is shown that the general recombination effect can be treated with in a similar manner as for air-filled ionization chambers, while there are currently no theories that adequately describe the initial recombination effect for LICs. Furthermore, the relationship between energy dependence and recombination losses in LICs are evaluated at different radiation qualities. Recently developed methods for the correction of general recombination losses in LICs are discussed and their validity evaluated.

  • 14.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Fällman, Erik
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Force measuring optical tweezers system for long time measurements of P pili stability2006In: Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues IV / [ed] Farkas, DL, Nicolau, DV, Leif, RC, 2006, Vol. 6088, p. 608810-Conference paper (Refereed)
    Abstract [en]

    A force-measuring optical tweezers instrumentation and long time measurements of the elongation and retraction of bacterial fimbriae from Uropathogenic E. coli (UPEC) under strain are presented. The instrumentation is presented in some detail. Special emphasis is given to measures taken to reduce the influence of noise and drifts in the system and from the surrounding, which makes long term force measurements possible. Individual P pili from UPEC bacteria were used as a biological model system for repetitive unfolding and refolding cycles of bacterial fimbriae under equilibrium conditions. P pili have evolved into a three-dimensional helix-like structure, the PapA rod, that can be successively and significantly elongated and/or unfolded when exposed to external forces. The instrumentation is used for characterization of the force-vs.-elongation response of the PapA rod of individual P pili, with emphasis on the long time stability of the forced unfolding and refolding of the helical structure of the PapA rod. The results show that the PapA rod is capable of withstanding extensive strain, leading to a complete unfolding of the helical structure, repetitive times during the life cycle of a bacterium without any noticeable alteration of the mechanical properties of the P pili. This function is believed to be importance for UPEC bacteria in vivo since it provides a close contact to a host cell (which is an initial step of invasion) despite urine cleaning attempts.

  • 15.
    Andersson, Magnus
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Svantesson, Mats
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Björnham, Oscar
    Swedish Defence Research Agency (FOI), SE-906 21 Umeå, Sweden.
    Badahdah, Arwa
    Department of Oral Biology, Boston University School of Dental Medicine.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Bullitt, Esther
    Department of Physiology and Biophysics, Boston University School of Medicine.
    A structural basis for sustained bacterial adhesion: Biomechanical properties of CFA/I Pili2012In: Journal of Molecular Biology, ISSN 0022-2836, E-ISSN 1089-8638, Vol. 415, no 5, p. 918-928Article in journal (Refereed)
    Abstract [en]

    Enterotoxigenic Escherichia coli (ETEC) are a major cause of diarrheal disease worldwide. Adhesion pili (or fimbriae), such as the CFA/I (colonization factor antigen I) organelles that enable ETEC to attach efficiently to the host intestinal tract epithelium, are critical virulence factors for initiation of infection. We characterized at single organelle level the intrinsic biomechanical properties and kinetics of individual CFA/I pili, demonstrating that weak external forces (7.5 pN) are sufficient to unwind the intact helical filament of this prototypical ETEC pilus and that it quickly regains its original structure when the force is removed. While the general relationship between exertion of force and an increase in the filament length for CFA/I pili associated with diarrheal disease is analogous to that of P-pili and type 1 pili, associated with urinary tract and other infections, the biomechanical properties of these different pili differ in key quantitative details. Unique features of CFA/I pili, including the significantly lower force required for unwinding, the higher extension speed at which the pili enter a dynamic range of unwinding, and the appearance of sudden force drops during unwinding can be attributed to morphological features of CFA/I pili including weak layer-to-layer interactions between subunits on adjacent turns of the helix, and the approximately horizontal orientation of pilin subunits with respect to the filament axis. Our results indicate that ETEC CFA/I pili are flexible organelles optimized to withstand harsh motion without breaking, resulting in continued attachment to the intestinal epithelium by the pathogenic bacteria that express these pili.

  • 16.
    Asadpoordarvish, Amir
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Functional and Flexible Light-Emitting Electrochemical Cells2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The introduction of artificial illumination has brought extensive benefits to mankind, and during the last years we have seen a tremendous progress in this field with the introduction of the energy-efficient light-emitting diode (LED) and the high-contrast organic LED display. These high-end technologies are, however, produced using costly and complex processes, and it is anticipated that the next big thing in the field will be the advent of a low-cost and “green” illumination technology, which can be fabricated in a cost- and material-efficient manner using non-toxic and abundant raw materials, and which features attractive form factors such as flexibility, robustness and light-weight. The light-emitting electrochemical cell (LEC) is a newly invented illumination technology, and in this thesis we present results that imply that it can turn the above vision into reality.

    The thin-film LEC comprises an active material sandwiched between a cathode and an anode as its key constituent parts. With the aid of a handheld air-brush, we show that functional large-area LECs can be fabricated by simply spraying three layers of solution -- forming the anode, active material, and cathode -- on top of a substrate. We also demonstrate that such “spray-sintered” LECs can feature multicolored emission patterns, and be fabricated directly on complex-shaped surfaces, with one notable example being the realization of a light-emission fork!

    Almost all LECs up-to-date have been fabricated on glass substrates, but for a flexible and light-weight emissive device, it is obviously relevant to identify more appropriate substrate materials. For this end, we show that it is possible to spray-coat the entire LEC directly on conventional copy paper, and that such paper-LECs feature uniform light-emission even under heavy bending and flexing.

    We have further looked into the fundamental aspects of the LEC operation and demonstrated that the in-situ doping formation, which is a characteristic and heralded feature of LECs, can bring problems in the form of doping-induced self-absorption. By quantitatively analyzing this phenomenon, we provided straightforward guidelines on how future efficiency-optimized LEC devices should be designed.

    The in-situ doping formation process brings the important advantage that LECs can be fabricated from solely air-stabile materials, but during light emission the device needs to be protected from the ambient air. We have therefore developed a functional glass/epoxy encapsulation procedure for the attainment of LEC devices that feature a record-long ambient-air operational lifetime of 5600 h. For the light-emission device of the future, it is however critical that the encapsulation is flexible, and in our last study, we show that the use of multi-layer barrier can result in high-performance flexible LECs.

  • 17.
    Asadpoordarvish, Amir
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. LunaLEC, Umeå, Sweden.
    Sandström, Andreas
    Larsen, Christian
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bollström, Roger
    Toivakka, Martti
    Österbacka, Ronald
    Edman, Ludvig
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Light-Emitting Paper2015In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 25, no 21, p. 3238-3245Article in journal (Refereed)
    Abstract [en]

    A solution-based fabrication of flexible and light-weight light-emitting devices on paper substrates is reported. Two different types of paper substrates are coated with a surface-emitting light-emitting electrochemical cell (LEC) device: a multilayer-coated specialty paper with an intermediate surface roughness of 0.4 μm and a low-end and low-cost copy paper with a large surface roughness of 5 μm. The entire device fabrication is executed using a handheld airbrush, and it is notable that all of the constituent layers are deposited from solution under ambient air. The top-emitting paper-LECs are highly flexible, and display a uniform light emission with a luminance of 200 cd m−2 at a current conversion efficacy of 1.4 cd A−1.

  • 18. Bae, Seung-Hee
    et al.
    Halperin, Daniel
    West, Jevin D.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Howe, Bill
    Scalable and Efficient Flow-Based Community Detection for Large-Scale Graph Analysis2017In: ACM Transactions on Knowledge Discovery from Data, ISSN 1556-4681, E-ISSN 1556-472X, Vol. 11, no 3, article id 32Article in journal (Refereed)
    Abstract [en]

    Community detection is an increasingly popular approach to uncover important structures in large networks. Flow-based community detection methods rely on communication patterns of the network rather than structural properties to determine communities. The Infomap algorithm in particular optimizes a novel objective function called the map equation and has been shown to outperform other approaches in third-party benchmarks. However, Infomap and its variants are inherently sequential, limiting their use for large-scale graphs. In this article, we propose a novel algorithm to optimize the map equation called RelaxMap. RelaxMap provides two important improvements over Infomap: parallelization, so that the map equation can be optimized over much larger graphs, and prioritization, so that the most important work occurs first, iterations take less time, and the algorithm converges faster. We implement these techniques using OpenMP on shared-memory multicore systems, and evaluate our approach on a variety of graphs from standard graph clustering benchmarks as well as real graph datasets. Our evaluation shows that both techniques are effective: RelaxMap achieves 70% parallel efficiency on eight cores, and prioritization improves algorithm performance by an additional 20-50% on average, depending on the graph properties. Additionally, RelaxMap converges in the similar number of iterations and provides solutions of equivalent quality as the serial Infomap implementation.

  • 19. Bae, Seung-Hee
    et al.
    Halperin, Daniel
    West, Jevin
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Howe, Bill
    Scalable Flow-Based Community Detection for Large-Scale Network Analysis2013In: 2013 IEEE 13TH INTERNATIONAL CONFERENCE ON DATA MINING WORKSHOPS (ICDMW) / [ed] Ding, W Washio, T Xiong, H Karypis, G Thuraisingham, B Cook, D Wu, X, IEEE, 2013, p. 303-310Conference paper (Refereed)
    Abstract [en]

    Community-detection is a powerful approach to uncover important structures in large networks. Since networks often describe flow of some entity, flow-based community-detection methods are particularly interesting. One such algorithm is called Infomap, which optimizes the objective function known as the map equation. While Infomap is known to be an effective algorithm, its serial implementation cannot take advantage of multicore processing in modern computers. In this paper, we propose a novel parallel generalization of Infomap called RelaxMap. This algorithm relaxes concurrency assumptions to avoid lock overhead, achieving 70% parallel efficiency in shared-memory multicore experiments while exhibiting similar convergence properties and finding similar community structures as the serial algorithm. We evaluate our approach on a variety of real graph datasets as well as synthetic graphs produced by a popular graph generator used for benchmarking community detection algorithms. We describe the algorithm, the experiments, and some emerging research directions in high-performance community detection on massive graphs.

  • 20.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Bernhardsson, Sebastian
    Umeå University, Faculty of Science and Technology, Physics.
    Equilibrium solution to the lowest unique positive integer game2010In: Fluctuation and Noise Letters, ISSN 0219-4775, E-ISSN 1793-6780, Vol. 9, no 1, p. 61-68Article in journal (Refereed)
    Abstract [en]

    We address the equilibrium concept of a reverse auction game so that no one can enhance the individual payoff by a unilateral change when all the others follow a certain strategy. In this approach the combinatorial possibilities to consider become very much involved even for a small number of players, which has hindered a precise analysis in previous works. We here present a systematic way to reach the solution for a general number of players, and show that this game is an example of conflict between the group and the individual interests.

  • 21.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bernhardsson, Sebastian
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Zipf's law unzipped2011In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 13, p. 043004-Article in journal (Refereed)
    Abstract [en]

    Why does Zipf's law give a good description of data from seemingly completely unrelated phenomena? Here it is argued that the reason is that they can all be described as outcomes of a ubiquitous random group division: the elements can be citizens of a country and the groups family names, or the elements can be all the words making up a novel and the groups the unique words, or the elements could be inhabitants and the groups the cities in a country, and so on. A Random Group Formation (RGF) is presented from which a Bayesian estimate is obtained based on minimal information: it provides the best prediction for the number of groups with $k$ elements, given the total number of elements, groups, and the number of elements in the largest group. For each specification of these three values, the RGF predicts a unique group distribution $N(k)\propto \exp(-bk)/k^{\gamma}$, where the power-law index $\gamma$ is a unique function of the same three values. The universality of the result is made possible by the fact that no system specific assumptions are made about the mechanism responsible for the group division. The direct relation between $\gamma$ and the total number of elements, groups, and the number of elements in the largest group, is calculated. The predictive power of the RGF model is demonstrated by direct comparison with data from a variety of systems. It is shown that $\gamma$ usually takes values in the interval $1\leq\gamma\leq 2$ and that the value for a given phenomena depends in a systematic way on the total size of the data set. The results are put in the context of earlier discussions on Zipf's and Gibrat's laws, $N(k)\propto k^{-2}$ and the connection between growth models and RGF is elucidated.

  • 22.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kim, Beom Jun
    Dept. of Physics, Sungkyunkwan Univ., Suwon, Korea.
    Numerical Study of Game Theory2010In: New Physics, ISSN 0374-4914, Vol. 60, no 9, p. 943-951Article in journal (Other academic)
    Abstract [en]

    Game-theoretic approach has been providing a powerful tool in qualitative understanding of macroscopic social phenomena in social sciences, e.g., in economics and political science. Recently, researchers in physics, especially in statistical physics, use these game-theoretic approaches but in more quantitative way and have been producing a variety of interesting results in the new research area called ’sociophysics’ by studying human society as a complex system. This work introduces recent works that have tackled combinatorial complexities arising in game-theoretic studies with the aid of simplified assumptions and numerical computations. We first show how cooperation emerges in the prisoner’s dilemma game when each player’s memory capacity is enhanced and suggest that the intelligent tit-for-tat strategy plays a crucial role in the history of cooperation. And then it is numerically shown that there is a certain case of simultaneous coordination among many players where the system has a high risk of failure when everyone is willing to follow the coordination, which is actually higher than when some are not concerned about it. Lastly, we discuss mathematical treatment of an equilibrium solution for a reverse auction game, which is a variant of the minority game, and its computational approach.

  • 23.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Non-Kosterlitz-Thouless transitions for the q-state clock models2010In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 82, no 3, p. 031102-Article in journal (Refereed)
    Abstract [en]

    The $q$-state clock model with the cosine potential has a single phasetransition for $q\leq4$ and two transitions for $q\geq5$. It is shown byMonteCarlo simulations that the helicity modulus for the five-state clock model($q=5$) does not vanish at the high-temperature transition. This is incontrast to the clock models with $q\geq6$ for which the helicity modulusvanishes. This means that the transition for the five-state clock modeldiffers from the Kosterlitz-Thouless (KT) transition. It is also shown thatthis change in the transition is caused by an interplay between the numberof angular directions and the interaction potential: by slightly modifyingthe interaction potential, the KT transition for $q=6$ turns into the samenon-KT transition. Likewise, the KT transition is recovered for $q=5$ whenthe Villain potential is used. Comparisons with other clock-model resultsare made and discussed.

  • 24.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Physics.
    Bernhardsson, Sebastian
    Umeå University, Faculty of Science and Technology, Physics.
    Choi, Kweon
    Gyeonggi Science High School.
    Kim, Beom Jun
    Department of Energy Science and BK21 Physics Research Division, Sungkyunkwan University, Suwon 440-746, Korea.
    Flow improvement caused by agents who ignore traffic rules2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 80, no 1, p. 016111-Article in journal (Refereed)
    Abstract [en]

    A system of agents moving along a road in both directions is studied numerically within a cellular-automata formulation. An agent steps to the right with probability $q$ or to the left with $1-q$ when encountering other agents. Our model is restricted to two agent types, traffic-rule abiders ($q=1$) and traffic-rule ignorers ($q=1/2$). The traffic flow, resulting from the interaction between these two types of agents, is obtained as a function of density and relative fraction. The risk for jamming at a fixed density, when starting from a disordered situation, is smaller when every agent abides by a traffic rule than when all agents ignore the rule. Nevertheless, the absolute minimum occurs when a smallfraction of ignorers are present within a majority of abiders. The characteristic features for the spatial structure of the flow pattern are obtained and discussed.

  • 25.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Kim, Beom Jun
    Department of Physics, Sungkyunkwan University, Suwon 440-746, Republic of Korea.
    The Ten Thousand Kims2011In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 13, p. 073036-Article in journal (Refereed)
    Abstract [en]

    In the Korean culture the family members are recorded in special familybooks. This makes it possible to follow the distribution of Korean familynames far back in history. It is here shown that these name distributionsare well described by a simple null model, the random group formation (RGF)model. This model makes it possible to predict how the name distributionschange and these predictions are shown to be borne out. In particular, theRGF model predicts that, for married women entering a collection of familybooks in a certain year, the occurrence of the most common family name``Kim'' should be directly proportional the total number of married womenwith the same proportionality constant for all the years. This prediction isalso borne out to high degree. We speculate that it reflects some inherentsocial stability in the Korean culture. In addition, we obtain an estimate ofthe total population of the Korean culture down to year 500 AD, based on theRGF model and find about ten thousand Kims.

  • 26.
    Baek, Seung Ki
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Shima, Hiroyuki
    Department of Applied Physics, Graduate School of Engineering, Hokkaido University, Sapporo 060-8628, Japan.
    Kim, Beom Jun
    BK21 Physics Research Division and Department of Energy Science, Sungkyunkwan University, Suwon 440-746, Korea.
    Curvature-induced frustration in the XY model on hyperbolic surfaces2009In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 79, no 6, p. 060106(R)-Article in journal (Refereed)
    Abstract [en]

    We study low-temperature properties of the XY spin model on a negatively curved surface. Geometric curvature of the surface gives rise to frustration in local spin configuration, which results in the formation of high-energy spin clusters scattered over the system. Asymptotic behavior of the spin-glass susceptibility suggests a zero-temperature glass transition, which is attributed to multiple optimal configurations of spin clusters due to nonzero surface curvature of the system. It implies that a constant ferromagnetic spin interaction on a regular lattice can exhibit glasslike behavior without possessing any disorder if the lattice is put on top of a negatively curved space such as a hyperbolic surface.

  • 27. Barbercheck Epler, Chelsea R.
    et al.
    Bullitt, Esther
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bacterial adhesion pili2018In: Membrane protein complexes: structure and function / [ed] J. Robin Harris, Egbert Boekema, Springer Publishing Company, 2018, , p. 18p. 1-18Chapter in book (Refereed)
    Abstract [en]

    Escherichia coli bacterial cells produce multiple types of adhesion pili that mediate cell-cell and cell-host attachments. These pili (also called 'fimbriae') are large biopolymers that are comprised of subunits assembled via a sophisticated micro-machinery into helix-like structures that are anchored in the bacterial outer membrane. They are commonly essential for initiation of disease and thus provide a potential target for antibacterial prevention and treatment. To develop new therapeutics for disease prevention and treatment we need to understand the molecular mechanisms and the direct role of adhesion pili during pathogenesis. These helix-like pilus structures possess fascinating and unique biomechanical properties that have been thoroughly investigated using high-resolution imaging techniques, force spectroscopy and fluid flow chambers. In this chapter, we first discuss the structure of pili and the micro-machinery responsible for the assembly process. Thereafter, we present methods for measurement of the biomechanics of adhesion pili, including optical tweezers. Data demonstrate unique biomechanical properties of pili that allow bacteria to sustain binding during in vivo fluid shear forces. We thereafter summarize the current biomechanical findings related to adhesion pili and show that pili biomechanical properties are niche-specific. That is, the data suggest that there is an organ-specific adaptation of pili that facilitates infection of the bacteria's target tissue. Thus, pilus biophysical properties are an important part of Escherichia coli pathogenesis, allowing bacteria to overcome hydrodynamic challenges in diverse environments.

  • 28. Bech, Morten L
    et al.
    Bergstrom, Carl T
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Garratt, Rodney J
    Mapping change in the overnight money market2015In: Physica A: Statistical Mechanics and its Applications, ISSN 0378-4371, E-ISSN 1873-2119, Vol. 424, p. 44-51Article in journal (Refereed)
    Abstract [en]

    We use an information-theoretic approach to describe changes in lending relationships between financial institutions around the time of the Lehman Brothers failure. Unlike previous work that conducts maximum likelihood estimation on undirected networks our analysis distinguishes between borrowers and lenders and looks for broader lending relationships (multi-bank lending cycles) that extend beyond the immediate counter-parties. We detect significant changes in lending patterns following implementation of the Interest on Required and Excess Reserves policy by the Federal Reserve in October 2008. Analysis of micro-scale rates of change in the data suggests these changes were triggered by the collapse of Lehman Brothers a few weeks before.

  • 29.
    Berggren, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wave study Seaflex mooring system: Wave study to illuminate how first and second order wave force transfer to and affects the loading of flexible Seaflex mooring system2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    When constructing a marina, one must consider many factors for calculating the mooring forces transferred to the mooring system of the docks. The forces transferred from waves is of course one of the most important. The wave induced forces may be described in different orders, the first-order wave forces from the frequency domain and the second-order wave forces determined from a wave field of different standing waves acting together. All floating objects are subjected to these wave forces, but for different mooring systems the transferred mooring force may vary. To describe the need for different calculations depending on the mooring system, a comparison to a spring system is made for both a Seaflex hawser and a guided pile system, which illustrates a significant difference in transferred mooring load. This is due to the hysteresis giving a low spring constant to the Seaflex hawser, which in turn transfers very little of the frequency induced first-order forces to the mooring system. This gives the conclusion that different methods for scaling the Seaflex mooring system is needed, since the first-order wave forces are not as significant than for a semi-rigid mooring system.

  • 30.
    Berglund, Tomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Ice fracture model for real-time shipsimulator2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Navigating in the arctic has become more common, but it is dicult and dangerousdue to the presence of ice. Any training under safer circumstances is therefore veryvaluable, enter the need for ship simulators. Ship simulators today incorporate manyfeatures, such as cranes, anchors, wires, and state of the art physics. However, theinclusion of ice is very rare due to the complexity of simulating the feedback from theice breaking progress.The purpose of this project is to build a model and numerical methods to simulate icefracture in real-time, which is to be used in ship simulators. The model presented inthis project is implemented with the use of the physics engine AgX Multiphysics madeby Algoryx Simulation ABThe method represents the ice sheet as a non-homogeneous mesh. A collision with thehull of the ship injects deformation energy into the ice. The energy from the inelasticimpact is distributed on the ice sheet according to a quasi-static crack propagationmodel that is dened on a static mesh. The cracks are guided using stress elds thatapproximate the strain in each vertex. The distribution of the strain is done by a simplemodel which allows for breaking ice in non-uniform fragments. This is more realisticthan fracture in predened shapes which is the main contribution of this project. Thefragments become unbreakable rigid body ice oes that interact with the ship's hull bycollision and friction.The implementation of the ice model is tested by using a trimesh model of the TorViking II icebreaker using approximated buoyancy calculations, damping equations,and engine forces.Real-time performance is not achieved yet in the general case, but this is due to thechoice of collision geometry and the oe creation. Unstable force spikes from thecontacts between the ship and the ice is detected, but the overall global ice resistanceshows few abnormalities. Replacing the collision geometry and the rigid body oes isnecessary for the implementation to be able to run in real-time. Further experimentsto compare with real model data is needed to be able to validate the model.

  • 31.
    Bergström, Christina
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Computational Fluid Dynamic Analysis of Effects of Local Geometry & Bathymetry on Tidal Turbine Performance2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The power output from tidal turbines is examined due to the influences of bathymetry effects and beforehand believed beneficial arrays of tidal turbines. Additionally the velocity profile behaviour over bathymetry differences is investigated by applying a 1/7th power law approximating the inlet velocity profile. This report describes the complete work from the beginning of building up bathymetry and multi device models, through serious analysis of interesting results achieved. The models are built in the commercial software of ANSYS DesignModelerTM and further simulated by using the CFD code of ANSYS FluentTM 14.5. The turbine(s) is approximated by an actuator disk(s) and the method of porous media conditions. The turbulence model applied is the RANS k-ω SST.The project consists of two preliminary studies (the model study and the mesh study) and two main studies (the multi device study and the bathymetry study). The main studies are done in parallel to each other independently, examining which parameters that have influence of the total power output. However the studies are aiming in the same direction of the end goal; the gained knowledge is to be used for bonding the studies into one in future work.The multi device study focuses on the parameter of lateral and longitudinal spacing between several deployed turbines, and investigates mainly 4 configurations consisting of 4 numbers of turbines each. Two additional configurations are investigated which consists of 3 respective 5 number of turbines. The inlet boundary conditions are set to total pressure inlet. No bathymetry is added.The bathymetry study focuses on the parameter of how bathymetry differences, designed from an exact defined gaussian curve, influences the total power output from the turbines. The bathymetry differences are varied with a bump and a trough of two different dimensions, 3 [m] and 6 [m] respectively. Additionally the bathymetry study considers the velocity profiles behaviour over bathymetry differences through the 1/7th power law profile applied at the inlet boundary condition. In total the bathymetry study consists of 14 models; 4 flat models, 6 bump models and 4 trough models with and without turbine respectively.The results from the multi device study strongly indicate that both lateral and longitudinal spacing is important for setting up configuration patterns. It is shown that at several lateral spacing dimensions, a velocity increase between the turbines occur, which could be used in a beneficial purpose for a second row of turbines.The result from the bathymetry study indicates that placing a turbine on top of a bump contributes to a higher power output, while placing a turbine in a trough indicates that, due to flow separation the attack velocity into the turbine becomes remarkable low and gives a much lower power output. Furthermore it is concluded that already at bathymetry differences of 3 [m] of magnitude, the velocity behaviour and total power output is influenced. Particularly there are interesting results shown for the trough models of 6 [m] of magnitude while separation phenomena occurs with a large influence of the turbines ability of power delivery.The results from the velocity profile investigation shows interesting results of non-symmetric behaviour over bathymetry differences, which are important results for future elaboration set ups. The non-symmetric behaviour is, notable, much larger at 6 [m] of magnitude comparing with 3 [m].Additionally a large work is done on analysing the theoretical number of maximal power outtake possible. There are to date no theoretical number determined for the maximum power coefficient Cp for under water turbines, corresponding to the known Betz’s limit valid above water surface i.e. used in wind industry. The concluded results are determined to be left out as an open discussion in Appendix inside this report.

  • 32.
    Bernhardsson, Sebastian
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rocha, Luis E C
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Minnhagen, Petter
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Size dependent word frequencies and translational invariance of books2010In: Physica A: Statistical Mechanics and its Applications, ISSN 0378-4371, E-ISSN 1873-2119, Vol. 389, no 2, p. 330-341Article in journal (Refereed)
    Abstract [en]

    It is shown that a real novel shares many characteristic features with a null model in which the words are randomly distributed throughout the text. Such a common feature is a certain translational invariance of the text. Another is that the functional form of the word-frequency distribution of a novel depends on the length of the text in the same way as the null model.This means that an approximate power-law tail ascribed to the data will have an exponent which changes with the size of the text-section which is analyzed.A further consequence is that a novel cannot be described by text-evolution models like the Simon model.The size-transformation of a novel is found to be well described by a specific Random Book Transformation.This size transformation in addition enables a more precise determination of the functional form of the word-frequency distribution.The implications of the results are discussed.

  • 33.
    Berthon, Beatrice
    et al.
    Wales Research and Diagnostic PET Imaging Centre, Cardiff University, Cardiff, UK.
    Häggström, Ida
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Apte, Aditya
    Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, USA.
    Beattie, Bradley J.
    Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, USA.
    Kirov, Assen S.
    Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, USA.
    Humm, John L.
    Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, USA.
    Marshall, Christopher
    Wales Research and Diagnostic PET Imaging Centre, Cardiff University, Cardiff, UK.
    Spezi, Emiliano
    School of Engineering, Cardiff University, Cardiff, Wales, UK.
    Larsson, Anne
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Schmidtlein, C. Ross
    Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, USA.
    PETSTEP: generation of synthetic PET lesions for fast evaluation of segmentation methods2015In: Physica medica (Testo stampato), ISSN 1120-1797, E-ISSN 1724-191X, Vol. 31, no 8, p. 969-980Article in journal (Refereed)
    Abstract [en]

    Purpose: This work describes PETSTEP (PET Simulator of Tracers via Emission Projection): a faster and more accessible alternative to Monte Carlo (MC) simulation generating realistic PET images, for studies assessing image features and segmentation techniques.

    Methods: PETSTEP was implemented within Matlab as open source software. It allows generating threedimensional PET images from PET/CT data or synthetic CT and PET maps, with user-drawn lesions and user-set acquisition and reconstruction parameters. PETSTEP was used to reproduce images of the NEMA body phantom acquired on a GE Discovery 690 PET/CT scanner, and simulated with MC for the GE Discovery LS scanner, and to generate realistic Head and Neck scans. Finally the sensitivity (S) and Positive Predictive Value (PPV) of three automatic segmentation methods were compared when applied to the scanner-acquired and PETSTEP-simulated NEMA images.

    Results: PETSTEP produced 3D phantom and clinical images within 4 and 6 min respectively on a single core 2.7 GHz computer. PETSTEP images of the NEMA phantom had mean intensities within 2% of the scanner-acquired image for both background and largest insert, and 16% larger background Full Width at Half Maximum. Similar results were obtained when comparing PETSTEP images to MC simulated data. The S and PPV obtained with simulated phantom images were statistically significantly lower than for the original images, but led to the same conclusions with respect to the evaluated segmentation methods.

    Conclusions: PETSTEP allows fast simulation of synthetic images reproducing scanner-acquired PET data and shows great promise for the evaluation of PET segmentation methods.

  • 34. Biryulin, YF
    et al.
    Kurdybaylo, D
    Shamanin, V
    Aleksjuk, G
    Volkova, T
    Melenevskaya, E
    Saydashev, I
    Eidelman, E
    Makarova, Tatiana
    Ioffe Physico-Technical Institute RAS, Russia.
    Terukov, E
    Zaitseva, N
    Negrov, V
    Tkatchyov, A
    Strongly non-linear carbon nanofibre influence on electrical properties of polymer composites2008In: Fullerenes, nanotubes, and carbon nanostructures (Print), ISSN 1536-383X, E-ISSN 1536-4046, Vol. 16, no 5-6, p. 629-633Article in journal (Refereed)
    Abstract [en]

    Composites of carbon nanofibres (CNF) (30-50 nm diam., length up to 1 mu m) in two polymer matrices (polybutadiene-styrene and polypyrrhol) show strong non-linearities of conductivity vs. CNF concentration. We have studied their voltage-current dependencies, and observed correlation of their extrema and layer morphology. Multistability of conductivity is discovered, with apparent effect of magnetic field effect on it in polypyrrhol-based composites. In addition CNF spatial configuration influence on layers' conductivity is discussed.

  • 35.
    Björklund, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    A Hierarchical POD Reduction Method of Finite Element Models with Application to Simulated Mechanical Systems2012Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    When simulating mechanical systems the flexibility of the components often has to be taken into account. This is particularly important for simulations when high detailed information is demanded, e.g. to calculate stresses. To this end the Finite Element Method (FEM) is often used. However the models can become very large, containing millions of degrees of freedom. Solving large linear systems are computationally demanding. Therefore ways of reducing the problem is often sought. These reduction does, however, remove much of the details that was to be investigated. In this thesis this problem is addressed by creating a reduction scheme, using Proper Orthogonal Decomposition (POD), that significantly reduces a problem but still captures much of the details. A novel method for enriching regular POD-based model reduction methods with hierarchically determined enrichment POD-modes is developed. The method is proposed and validated in a FEM application towards dynamical simulation. The enriched method is compared against a regular POD reduction technique. An numerical study is made of a model example of linear elasticity in a gearwheel. The numerical study suggests that the error of displacements is around ten times smaller, on average, when using the enriched basis compared to a reference basis of equal dimensionality consisting of only regular POD modes. Also it is shown that local quantities as the von Mises stress in a gearwheel tooth is preserved much better using the enriched basis. An a posteriori error estimate is proposed and proved for the static case, showing that the error is bound.

  • 36.
    Björnham, Oscar
    et al.
    Swedish Defence Research Agency (FOI), Umeå, Sweden.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics. Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR).
    Theory for nonlinear dynamic force spectroscopy2017In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 46, no 3, p. 225-233Article in journal (Refereed)
    Abstract [en]

    Dynamic force spectroscopy (DFS) is an experimental technique that is commonly used to assess information on the strength, energy landscape, and lifetime of noncovalent bio-molecular interactions. DFS traditionally requires an applied force that increases linearly with time so that the bio-complex under investigation is exposed to a constant loading rate. However, tethers or polymers can modulate the applied force in a nonlinear manner. For example, bacterial adhesion pili and polymers with worm-like chain properties are structures that show nonlinear force responses. In these situations, the theory for traditional DFS cannot be readily applied. In this work, we expand the theory for DFS to also include nonlinear external forces while still maintaining compatibility with the linear DFS theory. To validate the theory, we modeled a bio- complex expressed on a stiff, an elastic, and a worm-like chain polymer, using Monte Carlo methods, and assessed the corresponding rupture force spectra. It was found that the nonlinear DFS (NLDFS) theory correctly predicted the numerical results. We also present a protocol suggesting an experimental approach and analysis method of the data to estimate the bond length and the thermal off-rate.

  • 37.
    Björnham, Oscar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Schedin, Staffan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Methods and error estimations of uncertainties in single-molecule dynamic force spectroscopy2009In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 38, no 7, p. 911-922Article in journal (Refereed)
    Abstract [en]

    In dynamic force spectroscopy, access to the characteristic parameters of single molecular bonds requires non-trivial measurements and data processing as the rupture forces are found not only to be distributed over a wide range, but are also dependent on the loading rate. The choice of measurement procedure and data processing methods has a considerable impact on the accuracy and precision of the final results. We analyse, by means of numerical simulations, methods to minimize and assess the magnitude of the expected errors for different combinations of experimental and evaluation methods. It was found that the choice of fitting function is crucial to extract correct parameter values. Applying a Gaussian function, which is a common practice, is equivalent to introducing a systematic error, and leads to a consequent overestimation of the thermal off-rate by more than 30%. We found that the precision of the bond length and the thermal off-rate, in presence of unbiased noise, were improved by reducing the number of loading rates for a given number of measurements. Finally, the results suggest that the minimum number of measurements needed to obtain the bond strength, with acceptable precision, exceeds the common number of ~100 reported in literature.

     

  • 38.
    Björnham, Oscar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Sundqvist, Tobias
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Measuring and modelling of humidity penetration in an electronic control unit2000Independent thesis Advanced level (degree of Master (One Year)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Real world modeling has become a very useful tool when new designs and applications are tested before they are introduced on the market. A field that recently has discovered the possible use of modeling is reliability prediction. The reliability and lifetime of a component has until recently been based on months and years of testing. In order to shorten the test time it is possible to simulate the environmental effect on the components. Another advantage of modeling is that changes of large systems where many different components work together can easily be studied. Without modeling the reliability has to be tested over and over again if the system is redesigned since it is impossible to know how the new change will affect the reliability.

    Since electronic circuits are being made smaller and smaller with the increasing demand of faster technology the circuits are very vulnerable to corrosion. A trend in the automotive industry is also to move the electronic devices from the benign environment in the cab to the hash environment on the driveline or the chassi. The most common way to protect the electronics from the hash environment is to put it into a protective covering, also called Electronic Control Unit (ECU). Even though the ECU is sealed, water can still enter the ECU in several ways and cause serious damages by corrosion. The corrosion rate of a component is among others depending of the environmental humidity and temperature. Knowing the humidity and temperature are therefore very important to be able to eliminate corrosion problems. In order to achieve a better understanding of the physics behind the failure and to improve the reliability of the ECU a model of the temperature and humidity penetration is built in this thesis.

    There are several components in the ECU which all responds differently to water vapour. By measuring the humidity penetration in the ECU while components were added one by one, the physical properties of the components could be determined. Some properties were also determined through additional solubility measurements. The humidity penetration of the ECU is then predicted by inserting these properties into mathematical models in SimulinkÓ.

    The conclusion is that it is possible to model the humidity penetration and the temperature changes in the ECU. After the physical properties of the components were determined, the diffusion model agreed well with measurements. The numerical method used in this thesis has been found to be fast and stable. The length of the time-steps has been varied from a couple of minutes to more than an hour in the numerical model. A few physical properties has to be examined more in detailed and the model is then going to be a good foundation on which corrosion and other damaging processes can be modelled.

  • 39.
    Blomquist, M
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Karlsson, Mikael
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Measured lung dose correction factors for 50 MV photons1998In: Physics in Medicine and Biology, ISSN 0031-9155, E-ISSN 1361-6560, Vol. 43, no 11, p. 3225-3234Article in journal (Refereed)
    Abstract [en]

    Some clinically relevant measurements of lung tissue/water equivalent interfaces have been performed for a 50 MV therapeutic x-ray beam. The purpose was to investigate the severity of dose perturbation effects in lung tissue and adjacent tissues using an energy well above the common clinical practice in thoracic irradiations. The phantoms were constructed of solid water, PMMA and white polystyrene as soft tissue (water) equivalents, and cork was used as the lung tissue equivalent. Measurements were performed using radiographic film and a cylindrical ionization chamber. The results show that the degradation of the 20/80% beam penumbra in the lung region is severe, up to 2.5 times the penumbra in water for a 10 cm thick lung with a density of 0.30 x 10(3) kg m(-3). The lack of electronic equilibrium in the low-density region can cause underdosage at the lung/tumour interface of up to 30% of maximum target dose, and the build-up depth to 95% of target dose in unit density tissue behind the lung may be as large as 22 mm. It is also shown that these figures strongly depend on patient anatomy and beam size and why a careful calculation of the individual dose distribution is needed for optimal choice of photon beam energy in thoracic treatments.

  • 40.
    Bodin, Madelen
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Winberg, Mikael
    Umeå University, Faculty of Science and Technology, Department of Science and Mathematics Education.
    Learning physics in a simulation environment2007Conference paper (Refereed)
  • 41.
    Bohlin, Ludvig
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Viamontes Esquivel, Alcides
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lancichinetti, Andrea
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Robustness of journal rankings by network flows with different amounts of memory2016In: Journal of the Association for Information Science and Technology, ISSN 2330-1635, E-ISSN 2330-1643, Vol. 67, no 10, p. 2527-2535Article in journal (Refereed)
    Abstract [en]

    As the number of scientific journals has multiplied, journal rankings have become increasingly important for scientific decisions. From submissions and subscriptions to grants and hirings, researchers, policy makers, and funding agencies make important decisions influenced by journal rankings such as the ISI journal impact factor. Typically, the rankings are derived from the citation network between a selection of journals and unavoidably depend on this selection. However, little is known about how robust rankings are to the selection of included journals. We compare the robustness of three journal rankings based on network flows induced on citation networks. They model pathways of researchers navigating the scholarly literature, stepping between journals and remembering their previous steps to different degrees: zero-step memory as impact factor, one-step memory as Eigenfactor, and two-step memory, corresponding to zero-, first-, and second-order Markov models of citation flow between journals. We conclude that higher-order Markov models perform better and are more robust to the selection of journals. Whereas our analysis indicates that higher-order models perform better, the performance gain for higher-order Markov models comes at the cost of requiring more citation data over a longer time period.

  • 42.
    Bradley, Michael
    et al.
    Umeå University, Faculty of Science and Technology, Physics.
    Eriksson, Daniel
    Umeå University, Faculty of Science and Technology, Physics.
    Fodor, Gyula
    Rácz, Isván
    Slowly and rigidly rotating perfect fluid balls of Petrov type D2008In: Proceedings of the Eleventh Marcel Grossmann Meeting on General Relativity, 2008, p. 795-806Conference paper (Refereed)
  • 43.
    Brännlund, Niklas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Modeling and implementation of dense gas effects in a Lagrangian dispersion model2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The use of hazardous toxic substances is very common in the industrial sector. The substances are often stored in tanks in storage compartments or transported between industrial premises. In case of an accident involving these substances, severe harm can affect both population and the environment. This leaves a demand for an accurate prediction of the substance concentration distribution to mitigate the risks as much as possible and in advance create suitable safety measures. Toxic gases and vapors are often denser than air making it affected by negative buoyancy forces. This will make the gas descend and spread horizontally when reaching the ground.

    Swedish Defence Research Agency (FOI) carries today a model called LillPello for simulating the dispersion of gases, yet it does not account for the specific case of a dense gas. Therefore, this thesis aims to implement the necessary effects needed to accurately simulate the dispersion of a dense gas. These effects were implemented in Fortran 90 by solving five conservation equations for energy, momentum (vertical and horizontal) and mass. The model was compared against experimental data of a leak of ammonia (NH3).

    By analyzing the result of the simulations in this thesis, we can conclude that the overall result is satisfactory. We can notice a small concentration underestimation at all measurement points and the model produced a concentration power law coefficient which lands inside the expected range. Two out of the three statistical quantities Geometric Mean (MG), Geometric Variance (VG) and Factor of 2 (FA2) produced values within the ranges of acceptable values. The drawback of the model as it is implemented today is its efficiency, so the main priority for the future of this thesis is to improve this. The model should also be analyzed on more experiments to further validate its accuracy.

  • 44. Bujila, Robert
    et al.
    Kull, Love
    Danielsson, Mats
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Applying three different methods of measuring CTDIfree air to the extended CTDI formalism for wide-beam scanners (IEC 60601-2-44): A comparative study.2018In: Journal of Applied Clinical Medical Physics, ISSN 1526-9914, E-ISSN 1526-9914Article in journal (Refereed)
    Abstract [en]

    PURPOSE: The weighted CT dose index (CTDI<sub>w</sub> ) has been extended for a nominal total collimation width (nT) greater than 40 mm and relies on measurements of CTDIfreeair. The purpose of this work was to compare three methods of measuring CTDIfreeair and subsequent calculations of CTDI<sub>w</sub> to investigate their clinical appropriateness.

    METHODS: The CTDIfreeair, for multiple nTs up to 160 mm, was calculated from (1) high-resolution air kerma profiles from a step-and-shoot translation of a liquid ionization chamber (LIC) (considered to be a dosimetric reference), (2) pencil ionization chamber (PIC) measurements at multiple contiguous positions, and (3) air kerma profiles obtained through the continuous translation of a solid-state detector. The resulting CTDIfreeair was used to calculate the CTDI<sub>w</sub> , per the extended formalism, and compared.

    RESULTS: The LIC indicated that a 40 mm nT should not be excluded from the extension of the CTDI<sub>w</sub> formalism. The solid-state detector differed by as much as 8% compared to the LIC. The PIC was the most straightforward method and gave equivalent results to the LIC.

    CONCLUSIONS: The CTDI<sub>w</sub> calculated with the latest CTDI formalism will differ most for 160 mm nTs (e.g., whole-organ perfusion or coronary CT angiography) compared to the previous CTDI formalism. Inaccuracies in the measurement of CTDIfreeair will subsequently manifest themselves as erroneous calculations of the CTDI<sub>w</sub> , for nTs greater than 40 mm, with the latest CTDI formalism. The PIC was found to be the most clinically feasible method and was validated against the LIC.

  • 45.
    Castelain, Mickael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Koutris, Efstratios
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Helixlike pili is a prerequisite of uropathogenic E. coli to adhere to host and withstand urine flow2009In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 38, p. S111-Article in journal (Other academic)
  • 46.
    Castelain, Mickael
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rouxhet, Paul G.
    Pignon, Frederic
    Magnin, Albert
    Piau, Jean-Michel
    Single-cell adhesion probed in-situ using optical tweezers: A case study with Saccharomyces cerevisiae2012In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 111, no 11, p. 114701-Article in journal (Refereed)
    Abstract [en]

    A facile method of using optical trapping to measure cell adhesion forces is presented and applied to the adhesion of Saccharomyces cerevisiae on glass, in contact with solutions of different compositions. Trapping yeast cells with optical tweezers (OT) is not perturbed by cell wall deformation or cell deviation from a spherical shape. The trapping force calibration requires correction not only for the hydrodynamic effect of the neighboring wall but also for spherical aberrations affecting the focal volume and the trap stiffness. Yeast cells trapped for up to 5 h were still able to undergo budding but showed an increase of doubling time. The proportion of adhering cells showed the expected variation according to the solution composition. The detachment force varied in the same way. This observation and the fact that the detachment stress was exerted parallel to the substrate surface point to the role of interactions involving solvated macromolecules. Both the proportion of adhering cells and the removal force showed a distribution which, in our experimental conditions, must be attributed to a heterogeneity of surface properties at the cell level or at the subcellular scale. As compared with magnetic tweezers, atomic force microscopy, and more conventional ways of studying cell adhesion (shear-flow cells), OT present several advantages that are emphasized in this paper. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4723566]

  • 47.
    Castelain, Mickaël
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Ehlers, Sarah
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Klinth, Jeanna
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lindberg, Stina
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Uhlin, Bernt Eric
    Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Fast uncoiling kinetics of F1C pili expressed by uropathogenic Escherichia coli are revealed on a single pilus level using force-measuring optical tweezers2011In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 40, no 3, p. 305-316Article in journal (Refereed)
    Abstract [en]

    Uropathogenic Escherichia coli (UPEC) expressvarious kinds of organelles, so-called pili or fimbriae, thatmediate adhesion to host tissue in the urinary tract throughspecific receptor-adhesin interactions. The biomechanicalproperties of these pili have been considered important forthe ability of bacteria to withstand shear forces from rinsingurine flows. Force-measuring optical tweezers have beenused to characterize individual organelles of F1C typeexpressed by UPEC bacteria with respect to such properties.Qualitatively, the force-versus-elongation response wasfound to be similar to that of other types of helix-like piliexpressed by UPEC, i.e., type 1, P, and S, with force-inducedelongation in three regions, one of which represents theimportant uncoiling mechanism of the helix-like quaternarystructure. Quantitatively, the steady-state uncoiling forcewas assessed as 26.4 ±1.4 pN, which is similar to those ofother pili (which range from 21 pN for SI to 30 pN for type 1).The corner velocity for dynamic response (1,400 nm/s) wasfound to be larger than those of the other pili (400–700 nm/sfor S and P pili, and 6 nm/s for type 1). The kinetics werefound to be faster, with a thermal opening rate of 17 Hz, afew times higher than S and P pili, and three orders ofmagnitude higher than type 1. These data suggest that F1Cpili are, like P and S pili, evolutionarily selected to primarilywithstand the conditions expressed in the upper urinary tract.

  • 48.
    Castelain, Mickaël
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Koutris, Efstratios
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Björnham, Oscar
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Schedin, Staffan
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Characterization of the Biomechanical Properties of T4 Pili Expressed by Streptococcus pneumoniae – A Comparison between Helix-like and Open Coil-like Pili2009In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 10, no 9-10, p. 1533-1540Article in journal (Refereed)
    Abstract [en]

    Bacterial adhesion organelles, known as fimbria or pili, are expressed by Gram–positive as well as Gram–negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by Gram–positive Streptococcus pneumoniae with respect to their biomechanicalproperties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by Gram–negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble. Open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached bydistributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins.

  • 49.
    Costa, Luciano da F
    et al.
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Oliveira Jr, Osvaldo N
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Travieso, Gonzalo
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Rodrigues, Francisco A
    Instituto de Ciencias Matematicas e de Computacao, Universidade de Sao Paulo.
    Villas Boas, Paulino R
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Antiqueira, Lucas
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Viana, Matheus P
    Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo.
    Rocha, Luis E C
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Analyzing and modeling real-world phenomena with complex networks: a survey of applications2011In: Advances in Physics, ISSN 0001-8732, E-ISSN 1460-6976, Vol. 60, no 3, p. 329-412Article, review/survey (Refereed)
    Abstract [en]

    The success of new scientific areas can be assessed by their potential in contributing to new theoretical approaches and in applications to real-world problems. Complex networks have fared extremely well in both of these aspects, with their sound theoretical basis being developed over the years and with a variety of applications. In this survey, we analyze the applications of complex networks to real-world problems and data, with emphasis in representation, analysis and modeling. A diversity of phenomena are surveyed, which may be classified into no less than 11 areas, providing a clear indication of the impact of the field of complex networks.

  • 50.
    Dahlberg, Tobias
    Umeå University, Faculty of Science and Technology, Department of Physics.
    The first order Raman spectrum of isotope labelled nitrogen-doped reduced graphene oxide2016Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The topic of this thesis is the study of nitrogen functionalities in nitrogen-doped reduced graphene oxide using Raman spectroscopy. Specifically, the project set out to investigate if the Raman active nitrogen-related vibrational modes of graphene can be identified via isotope labelling. Previous studies have used Raman spectroscopy to characterise nitrogen doped graphene, but none has employed the method of isotope labelling to do so. The study was conducted by producing undoped, nitrogen-doped and nitrogen-15-doped reduced graphene oxide and comparing the differences in the first-order Raman spectrum of the samples. Results of this study are inconclusive. However, some indications linking the I band to nitrogen functionalities are found. Also, a hypothetical Raman band denoted I* possibly related to \spt{3} hybridised carbon is introduced in the same spectral area as I. This indication of a separation of the I band into two bands, each dependent on one of these factors could bring clarity to this poorly understood spectral area. As the results of this study are highly speculative, further research is needed to confirm them and the work presented here serves as a preliminary investigation.

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