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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.

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  • 2.
    Adjeiwaah, Mary
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Garpebring, Anders
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Nyholm, Tufve
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Sensitivity analysis of different quality assurance methods for magnetic resonance imaging in radiotherapy2020In: Physics and Imaging in Radiation Oncology, E-ISSN 2405-6316, Vol. 13, p. 21-27Article in journal (Refereed)
    Abstract [en]

    Background and purpose: There are currently no standard quality assurance (QA) methods for magnetic resonance imaging (MRI) in radiotherapy (RT). This work was aimed at evaluating the ability of two QA protocols to detect common events that affect quality of MR images under RT settings.

    Materials and methods: The American College of Radiology (ACR) MRI QA phantom was repeatedly scanned using a flexible coil and action limits for key image quality parameters were derived. Using an exploratory survey, issues that reduce MR image quality were identified. The most commonly occurring events were introduced as provocations to produce MR images with degraded quality. From these images, detection sensitivities of the ACR MRI QA protocol and a commercial geometric accuracy phantom were determined.

    Results: Machine-specific action limits for key image quality parameters set at mean±3σ" role="presentation" style="box-sizing: border-box; margin: 0px; padding: 0px; display: inline-block; line-height: normal; font-size: 16.2px; word-spacing: normal; overflow-wrap: normal; white-space: nowrap; float: none; direction: ltr; max-width: none; max-height: none; min-width: 0px; min-height: 0px; border: 0px; position: relative;">mean±3σ were comparable with the ACR acceptable values. For the geometric accuracy phantom, provocations from uncorrected gradient nonlinearity effects and a piece of metal in the bore of the scanner resulted in worst distortions of 22.2 mm and 3.4 mm, respectively. The ACR phantom was sensitive to uncorrected signal variations, electric interference and a piece of metal in the bore of the scanner but could not adequately detect individual coil element failures.

    Conclusions: The ACR MRI QA phantom combined with the large field-of-view commercial geometric accuracy phantom were generally sensitive in identifying some common MR image quality issues. The two protocols when combined may provide a tool to monitor the performance of MRI systems in the radiotherapy environment.

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  • 3.
    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.

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  • 4.
    Ahlman, Björn
    Umeå University, Faculty of Science and Technology, Department of Physics.
    The Physics and Image Processing of Cryo-ElectronTomography and the Estimation of Resolution using the Programs MOTIONCOR2 1.0.2 and CTFFIND 4.1.82019Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    We present a brief overview of the physics of cryo-electron tomography (cryo-ET) and the Image Processing related to this field. This serves as an introduction for readers unfamiliar with cryo-ET and as a background to the second part of the report, which concerns the programs CTFFIND and MOTIONCOR2. We correct tiltseries for sample motion with two different settings with MOTIONCOR2: with (only) Global Motion Correction and with Global+Local Motion Correction (5x5 patches). Then, using CTFFIND, we estimate the resolution in the tiltseries for the data sets without Motion Correction, with (only) Global Motion Correction, and with Global+Local Motion Correction, and make an assessment of the reliability of CTFFIND as a program for estimating the resolution. A total of 410 images were analyzed (10 tiltseries of 41 images each). When considering mean resolutions, we find CTFFIND to be useful and reliable, particularly when differences in means are of interest (e.g. differences between angles or defoci). However, due to e.g. the sensitivity of CTFFIND with respect to input parameters, we conjecture that CTFFIND is less reliable when individual images are analyzed, particularly when absolute resolutions are of interest. Provided that CTFFIND is accurate enough for a statistical analysis with respect to resolution, which we believe it is, the average increase in resolution when (only) Global Motion Correction is used for tiltseries from -60° to 60° with defocus -3 μm is around 0.9 Å (246 images analyzed). For defocus -5 μm, the equivalent average increase in resolution is around 1.1 Å (164 images analyzed). Results indicate that resolution is roughly linearly proportional to the magnitude of the tiltangle. The average difference in resolution between data sets with (only) Global Motion Correction and Global+Local Motion Correction for both defocus -3 μm and -5 μm is 0.0 Å, for two significant figures. This suggests that the sample motion is predominantly Global. For defocus -3 μm and -5 μm, there is a confidence level of 95% that if only Global Motion Correction is applied to a large set of tiltseries, a majority of the images will have a resolution that is higher than the images in the same set to which Motion Correction has not been applied (when corresponding images are compared). In an equivalent statistical analysis, we can not claim that either “(only) Global Motion Correction” or “Global+Local Motion Correction” is superior.

  • 5.
    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. 

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  • 6.
    Alakpa, Enateri V.
    et al.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Bahrd, Anton
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wiklund, Krister
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Novikov, Lev N.
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Ljungberg, Christina
    Umeå University, Faculty of Medicine, Department of Surgical and Perioperative Sciences, Hand Surgery.
    Kelk, Peyman
    Umeå University, Faculty of Medicine, Department of Integrative Medical Biology (IMB).
    Bioprinted schwann and mesenchymal stem cell co-cultures for enhanced spatial control of neurite outgrowth2023In: Gels, E-ISSN 2310-2861, Vol. 9, no 3, article id 172Article in journal (Refereed)
    Abstract [en]

    Bioprinting nerve conduits supplemented with glial or stem cells is a promising approach to promote axonal regeneration in the injured nervous system. In this study, we examined the effects of different compositions of bioprinted fibrin hydrogels supplemented with Schwann cells and mesenchymal stem cells (MSCs) on cell viability, production of neurotrophic factors, and neurite outgrowth from adult sensory neurons. To reduce cell damage during bioprinting, we analyzed and optimized the shear stress magnitude and exposure time. The results demonstrated that fibrin hydrogel made from 9 mg/mL of fibrinogen and 50IE/mL of thrombin maintained the gel’s highest stability and cell viability. Gene transcription levels for neurotrophic factors were significantly higher in cultures containing Schwann cells. However, the amount of the secreted neurotrophic factors was similar in all co-cultures with the different ratios of Schwann cells and MSCs. By testing various co-culture combinations, we found that the number of Schwann cells can feasibly be reduced by half and still stimulate guided neurite outgrowth in a 3D-printed fibrin matrix. This study demonstrates that bioprinting can be used to develop nerve conduits with optimized cell compositions to guide axonal regeneration.

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  • 7.
    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.

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  • 8.
    Al-Latifi, Yasir
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Optimizing numerical modelling of quantum computing hardware2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Quantum computers are being developed to solve certain problems faster than classical computers. Instead of using classical bits, they use quantum bits (qubits) that utilize quantum effects. At Chalmers University of Technology, researchers have already built a quantum chip consisting of two superconducting transmon qubits and are trying to build systems with more qubits. To assist in that process, they make numerical simulations of the quantum systems. However, these simulations face an intrinsic computational limitation: the Hilbert space of the system grows exponentially with the number of qubits. In order to mitigate the problem: the simulations should be made as efficient as possible, by applying certain approximations, while still obtaining accurate results. The aim of this project is to compare several of these approximations, to see how accurate they are and how fast they run on a classical computer. This is done by modelling the qubits as quantum anharmonic oscillators and testing several cases: varying the energy levels of the qubits, increasing the number of qubits, and testing the rotating-wave approximation (RWA). These cases were tested by implementing two-qubit gates on the system. The simulations were all made using the Python library QuTiP. The results show that one should simulate using at least one energy level higher than the maximum energy level required for the gate to function. For larger systems, the RWA will make a big difference in simulation times, while still giving relatively accurate results. When using the RWA, the number of levels used does not seem to affect the results significantly and one could therefore use the lowest possible energy levels that can simulate the system. 

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  • 9.
    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
  • 10.
    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.

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    Ion recombination in liquid ionization chambers (kappa)
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    Ion recombination in liquid ionization chambers (omslag)
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    Ion recombination in liquid ionization chambers (spikblad)
  • 11.
    Andersson, Jonas
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Radiation Dosimetry for CBCT – Quality Control and Applied Dosimetry2015Conference paper (Other academic)
    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.

  • 12.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    Granberg, Christoffer
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Diagnostic Radiology.
    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 / ESI-0064, EuroSafe Imaging , 2018Conference paper (Refereed)
  • 13.
    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.

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  • 14.
    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.

  • 15.
    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.

  • 16.
    Andersson, Jonas
    et al.
    Umeå University, Faculty of Medicine, Department of Radiation Sciences, Radiation Physics.
    Pavlicek, William
    Al-Senan, Rani
    Bolch, Wesley
    Bosmans, Hilde
    Cody, Dianna
    Dixon, Robert
    Colombo, Paola
    Dong, Frank
    Edyvean, Sue
    Jansen, Jan
    Kanal, Kalpana
    Leng, Shuai
    Liang, Qing
    McCullough, Cynthia
    McDonagh, Ed
    McNitt-Gray, Michael
    Paden, Robert
    Rehani, Madan
    Samei, Ehsan
    Sechopoulos, Ioannis
    Supanich, Mark
    Theodorakou, Christine
    Tian, Xiaoyu
    Torresin, Alberto
    Trianni, Annalisa
    Zamora, David
    Zanca, Federica
    Estimating Patient Organ Dosewith Computed Tomography: A Review of Present Methodologyand Required DICOM Information: A Joint Report ofAAPM Task Group 246 and the European Federationof Organizations for Medical Physics (EFOMP)2019Report (Refereed)
    Abstract [en]

    The purpose of this report is (1) to summarize the current state of the art in estimating organ doses from CT examinations and (2) to outline a road map for standardized reporting of essential parameters necessary for estimation of organ doses from CT imaging in the DICOM standard. To address these purposes, the report includes a comprehensive discussion of (1) the various metrics, concepts, and methods that may be used to achieve estimates of patient organ dose and (2) the DICOM standard for CT.

    This Joint Report of the American Association of Physicists in Medicine (AAPM) Task Group 246 and the European Federation of Organizations for Medical Physics (EFOMP) contains three major sections and an appendix. Section 2 (with additional material in the appendix) provides a review of basic CT dosimetry metrics, their uses and limitations in the context of organ dosimetry, and the DICOM information currently associated with parameters that affect CT dose metrics and, consequently, organ dose estimates. Section 3 provides an overview of present and emerging organ dose estimation methods reported in the literature, e.g., for the lens of the eye, breast tissue, colon, and skin. Finally, the report concludes with section 4, which provides a discussion on the sources and magnitudes of uncertainty for different organ dose estimation methods.

    Ongoing efforts to facilitate routine standardized estimation of patient organ doses from CT are dependent, in large part, on the availability of the DICOM Radiation Dose Structured Report (RDSR), which provides a host of information pertinent to radiation dose calculations. This report, therefore, includes detailed information on DICOM header content in CT images and how it can be used in organ dose estimation. The RDSR markedly expands the abilities of the clinical medical physicist to estimate doses at the patient, device, and protocol level

  • 17.
    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.

  • 18.
    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.

  • 19.
    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.

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  • 20.
    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.

  • 21.
    Andersson, Sabina
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Simulation challenges in robotic grasping2021Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Grasping and dexterous manipulation is a huge area in the current robotic research field. Traditionally in industrial environments, robots are customized for a certain task and work well with repetitive movements where the entire process is predetermined and deterministic. The possibility for a robot to adapt to its surroundings and manipulate objects with unknown properties is very limited and requires new models and methods. It is advantageous to explore and test new algorithms and models in a simulated environment before building physical systems. This thesis focuses on making the development, design and control of dexterous robot hands easier by exploring the benefits and challenges to use simulation in Algoryx's physics engine AGX Dynamics for experimentation and evaluation of design, motion planning, contact models, geometry, etc. The goal is to simulate complex grasping situations in AGX Dynamics and to build knowledge about contact mechanics to fully capture the dynamics of grasping in simulation. The work consists of validating the simulation library with regards to fundamental physics characteristics involved in grasping by a series of benchmark tests. The validation process aims to verify the models and numerical methods in AGX Dynamics to ensure sim2real transfer. The work has exposed friction as one of the biggest challenges in simulation. Developments of the current friction models that better represent the reality have been implemented and tested in AGX. They both show promising results for further development.

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  • 22.
    Anthony, Tim
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Evaluating machine learning models for predicting glioma from single nucleotide polymorphism data2020Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Early detection of cancer is necessary to minimize mental and physical distress. Therefore, this report investigated the possibilities of using machine learning methods to detect glioma in an early stage. This by looking at genetic data from real patients. This data consists of more than 14 million genetic features called SNP:s, and is therefore considered highly dimensional. However, the question is if these genetic data can be used for prediction of glioma? 

     The approach used was to first reduce the dimension by methods such as weighted cosine similarities, PCA, undercomplete autoencoder, t-SNE and sum pooling. To make prediction, k-means, naive bayes, kNN and neural networks were used.

     The results of this study show that the methods mentioned above can be difficult to use in determining the risk of cancer. However, this may depend on the hyperparameters used in the models as these play a major role in performance. Some important hyperparameters were the number of nodes and layers in the undercomplete autoencoder and the neural network. Using too many nodes or layers may cause these models to overfit. Contrary, using too few nodes or layers may instead cause them to underfit. The perplexity in the t-SNE and the number of blocks in the sum pooling were also key parameters, these two hyperparameters were hard to tune well since the grid search was very costly time-wise.

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  • 23.
    Aoshima, Koji
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics. Komatsu Ltd..
    Fälldin, Arvid
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wadbro, Eddie
    Umeå University, Faculty of Science and Technology, Department of Computing Science. Karlstad University, Sweden.
    Servin, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics. Algoryx Simulation.
    Data-driven models for predicting the outcome of autonomous wheel loader operationsManuscript (preprint) (Other academic)
    Abstract [en]

    This paper presents a method using data-driven models for selecting actions and predicting the total performance of autonomous wheel loader operations over many loading cycles in a changing environment. The performance includes loaded mass, loading time, work. The data-driven models input the control parameters of a loading action and the heightmap of the initial pile state to output the inference of either the performance or the resulting pile state. By iteratively utilizing the resulting pile state as the initial pile state for consecutive predictions, the prediction method enables long-horizon forecasting. Deep neural networks were trained on data from over 10,000 random loading actions in gravel piles of different shapes using 3D multibody dynamics simulation. The models predict the performance and the resulting pile state with, on average, 95% accuracy in 1.2 ms, and 97% in 4.5 ms, respectively. The performance prediction was found to be even faster in exchange for accuracy by reducing the model size with the lower dimensional representation of the pile state using its slope and curvature. The feasibility of long-horizon predictions was confirmed with 40 sequential loading actions at a large pile. With the aid of a physics-based model, the pile state predictions are kept sufficiently accurate for longer-horizon use.

  • 24. Ari Noriega, Jorge
    et al.
    Zapata-Prisco, Charles
    Garcia, Hector
    Hernandez, Elkin
    Hernandez, Jose
    Martinez, Ricardo
    Santos-Santos, Javier H.
    Pablo-Cea, Jose D.
    Calatayud, Joaquín
    Umeå University, Faculty of Science and Technology, Department of Physics. Departamento de Biología y Geología, Física y Química inorgánica. ESCET., Universidad Rey Juan Carlos, Madrid, Spain.
    Does ecotourism impact biodiversity?: An assessment using dung beetles (Coleoptera: Scarabaeinae) as bioindicators in a tropical dry forest natural park2020In: Ecological Indicators, ISSN 1470-160X, E-ISSN 1872-7034, Vol. 117, article id 106580Article in journal (Refereed)
    Abstract [en]

    Ecotourism can be defined as an environmental activity that takes place in well-preserved areas for recreation and with the responsibility of promoting their conservation. Nowadays, ecotourism is seen as a friendly pastime, but it can potentially affect negatively community diversity and structure by a number of processes such as soil compaction, erosion, and habitat alteration, among many others. Nonetheless, there is hardly any information on the impact of ecotourism in the Tropical Dry Forests and protected areas of the Neotropical region. In an attempt to fill this knowledge gap, the effect of ecotourism was evaluated in a study of a Tropical Dry Forest in the Tayrona National Natural Park of Colombia using dung beetles as bioindicators. A large-scale sampling of three sites with different levels of tourism intensity (no tourism - NT, low tourism - LT, and high tourism - HT) was performed using pitfall tramps baited with human/pig dung during two climatic seasons (rainy and dry). A total of 3238 individuals belonging to nine genera and 15 species were collected. Significant differences in abun-dances, richness, and the Shannon Wiener diversity index were observed between areas with tourism and those without. These differences disappeared during the dry season in response to the strong reduction in species abundance and richness associated to that time of year. All areas maintained a homogeneous beetle structure in terms of functional groups present irrelevant of the intensity level of tourism. Beta diversity analysis shows that the dung beetle assemblage has a nested structure, indicating that the pressure exerted by tourism entails the loss of particular species. Our results advocate that it is necessary to implement conservation strategies in order to reduce the negative impact of tourism on the National Park's biodiversity.

  • 25.
    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.

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  • 26.
    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.

  • 27. Aslak, Ulf
    et al.
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lehmann, Sune
    Constrained information flows in temporal networks reveal intermittent communities2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 97, no 6, article id 062312Article in journal (Refereed)
    Abstract [en]

    Many real-world networks represent dynamic systems with interactions that change over time, often in uncoordinated ways and at irregular intervals. For example, university students connect in intermittent groups that repeatedly form and dissolve based on multiple factors, including their lectures, interests, and friends. Such dynamic systems can be represented as multilayer networkswhere each layer represents a snapshot of the temporal network. In this representation, it is crucial that the links between layers accurately capture real dependencies between those layers. Often, however, these dependencies are unknown. Therefore, current methods connect layers based on simplistic assumptions that do not capture node-level layer dependencies. For example, connecting every node to itself in other layers with the same weight can wipe out dependencies between intermittent groups, making it difficult or even impossible to identify them. In this paper, we present a principled approach to estimating node-level layer dependencies based on the network structure within each layer. We implement our node-level coupling method in the community detection framework Infomap and demonstrate its performance compared to current methods on synthetic and real temporal networks. We show that our approach more effectively constrains information inside multilayer communities so that Infomap can better recover planted groups in multilayer benchmark networks that represent multiple modeswith different groups and better identify intermittent communities in real temporal contact networks. These results suggest that node-level layer coupling can improve the modeling of information spreading in temporal networks and better capture intermittent community structure.

  • 28.
    Auroux, Etienne
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Solution-processed light-emitting electrochemical cells: challenges and opportunities2023Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Our world is filling up with electronics. High-tech gadgets are integrated everywhere, from smart fridges able to track expiry dates and food usage, to microchip implants that let us unlock doors and pay with our hands. As innovative as they are, these new products and the many more to come impose new requirements on materials and fabrication methods. For instance, emerging electronic technologies that deliver light emission such as smart labels, authenticity features and light-based medical therapies, are often required to be flexible, see-through and low-cost, and in addition sustainable to fabricate, operate and recycle.

    In response to these challenges, the light-emitting industry is turning to organic electronics for solutions, a field that promises resource-efficient fabrication using environmentally benign materials. An interesting proposal is that of the light-emitting electrochemical cell (LEC), which, thanks to its simple structure, is well suitedfor high-throughput fabrication. The LEC is in many aspects a smart device, able to reorganize itself during operation via the electrochemical action of mobile ions, which create the injection and transport layers that require additional fabrication steps in other technologies. This elegant behavior makes the LEC tolerant to a large array of materials and fabrication methods, and hence a good fit for many applications.

    Yet the LEC is still today a scientific curiosity rather than an actual commercial solution and among the very few prototypes available on the market, none are able to meet the combined performance, resource efficiency and sustainability criteria. As a matter of fact, of the three layers that make an LEC, i.e., two electrodes surrounding an active material, only the later meet these requirements thanks to a strong recent research effort. In comparison, the electrodes have received little attention and are almost exclusively comprising metals or metal oxides deposited by time- and energy-expensive fabrication methods, making the LEC as a whole unfit for many applications.

    In an effort to push the LEC toward the untapped commercial niche of low-cost lighting, we tackle the problem of electrode fabrication with resource-efficiency in mind. We first show that up-scalable spray coating of inks under ambient air is a viable mean of fabrication for both active materials and electrodes alike. However, in doing so, we find that we create electrode interfaces that are open to ion transfer; an up-to-now overlooked issue that needs careful consideration when designing solution-processed LECs. Building on our discovery, we demonstrate that it is possible to fabricate an LEC entirely by using spray coating metal-free and organic inks; thereby demonstrating that an all-organic, metal-free and resource-efficient LEC is possible.

    I hope that our efforts will encourage others to work on solution-processed LECs, electrodes included, and develop ready-to-use products.

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  • 29.
    Auroux, Etienne
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Huseynova, Gunel
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Ràfols-Ribé, Joan
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Miranda la Hera, Vladimir
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Edman, Ludvig
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Metal-free and transparent light-emitting devices fabricated by sequentialspray coatingManuscript (preprint) (Other academic)
  • 30. 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.

  • 31. 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.

  • 32.
    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.

  • 33.
    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, 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.

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    Zipf's law unzipped
  • 34.
    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.

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    FULLTEXT02
  • 35.
    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.

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    FULLTEXT02
  • 36.
    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.

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    FULLTEXT01
  • 37.
    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, 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.

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  • 38.
    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.

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    FULLTEXT01
  • 39.
    Baigmohammadi, Mohammadreza
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Roussel, Olivier
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Dion, Claude
    Umeå University, Faculty of Science and Technology, Department of Physics.
    A Numerical Study of Lean Propane-Air Flame Acceleration at the Early Stages of Burning in Cold and Hot Isothermal Walled Small-Size Tubes2020In: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 104, no 1, p. 179-207Article in journal (Refereed)
    Abstract [en]

    In this study, the problem of lean propane-air premixed flame acceleration from closed to open end during the early stages of burning in small-size tubes with isothermal walls was considered. In particular, the effects of tube radius, slip/non-slip wall conditions, and the wall temperature on the flame propagation and shape were investigated numerically. Five stages of flame propagation are identified: 1) spherical expansion of the flame front; 2) finger shape expansion of the flame front before touching the wall; 3) flame propagation in the tube subjected to flame-wall interactions; 4) transformation of the flame shape into tulip form; 5) conversion of the tulip shape flame to finger. Our results show that the tube radius, wall condition and its temperature significantly affect flame propagation regimes even in the first instance of the flame propagation in the tubes. We find that increasing tube radius has, overall, the effect of increasing the flame propagation speed in isothermal tubes. Also, depending on tube radius and wall condition, the wall temperature can increase or decrease the flame propagation speed in the isothermal tubes. Furthermore, the results demonstrate that imposing either slip or non-slip condition on the tube’s walls impressively affects flame acceleration and its configuration in the early stages. We observe that, unlike flame propagation forms in the tubes with slip walls, the early exponential flame propagation phase in the tubes was generally followed by a linear flame propagation phase in the tubes with a non-slip wall condition. We obtain that flame propagation in tubes with slip wall conditions are more sensitive to variations in tube radius and wall temperature compared to non-slip conditions. We also see that, contrary to the exponential flame propagation phase, increasing the non-slip wall temperature reduces the flame propagation speed in the linear part of the flame propagation, while such an increase in temperature leads to oscillations in the flame propagation speed in the tubes with slip walls.

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  • 40. Baker, Joseph
    et al.
    Dahlberg, Tobias
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bullitt, Esther
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion pili to stress2021In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 118, no 21, article id e2023595118Article in journal (Refereed)
    Abstract [en]

    Escherichia coli express adhesion pili that mediate attachment to host cell surfaces and are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow forces, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that Class 1a pili of uropathogenic E. coli (UPEC), as well as Class 1b of enterotoxigenic E. coli (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC Class 5 pili. Examining structural and steered molecular dynamics simulation data, we find this difference in Class 1 pili subunit behavior originates from an alpha-helical motif that can unfold when exposed to force. A disulfide bond cross-linking beta-strands in Class 1 pili stabilizes subunits, allowing them to tolerate higher forces than Class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche since resident bacteria are exposed to stronger, more transient drag forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, Class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of Class 5 ETEC pili.

  • 41. Baker, Joseph
    et al.
    Dahlberg, Tobias
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bullitt, Esther
    Andersson, Magnus
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Unveiling the Contributions of Secondary Structure and Disulfide Bonds for Bacterial Adhesion Pili Extension using a Multiscale Approach2021Conference paper (Other academic)
    Abstract [en]

    Bacterial adhesion pili are essential virulence factors for many pathogenic Escherichia coli, including bacteria that cause urinary tract infections (UPEC) and diarrheal diseases (ETEC). To sustain adhesion under forces similar to those in the fluid environments of the urinary tract and gastrointestinal tract, these pili (also called fimbriae) can extend to over seven times their original length. Both UPEC and ETEC can uncoil their quaternary structure under pulling force and re-coil to their helical form when the force is reduced, as observed using optical tweezers. However, after extension to a linear polymer UPEC undergo an additional reversible conformational change, that is not seen in ETEC. The mechanism for this conformational change in UPEC is not known. Therefore, to obtain a comprehensive picture of pilus extension we have taken a synergistic approach that combines optical tweezer experiments, structural data from cryo-EM, and steered molecular dynamics simulations to investigate the response of pilin subunits to force.

    Our multi-faceted approach provides novel molecular-scale insights into the structural changes that occur in UPEC and ETEC pili under pulling forces. We find that the conformational change observed in UPEC pili in optical tweezer experiments is correlated with the presence of an alpha helix. In addition, structural analysis and steered molecular dynamics simulations show that there is a disulfide bond that provides additional stability of UPEC pilin subunits that is not observed in ETEC pilins, which lack cysteine residues. Together, these results suggest that the mechanism of extension of bacterial adhesion pili is related to their environmental niche, and the magnitude of fluid forces in the urinary tract versus the GI tract.

  • 42. 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.

  • 43. 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.

  • 44.
    Berggren, Alexander
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Development of a Mobile Reactor for Large Scale Water Treatment2019Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Water pollution is one of many environmental problems that currently exists and inadequate treatment of industrial wastewater is contributing to further pollution. SpinChem AB's Rotating Bed Reactor (RBR) technology offers the possibility of water treatment by carrying out reactions between a solution and a solid phase. To move further in the field of large scale water treatment, SpinChem AB developed a prototype of a mobile reactor, i.e. a raft, carrying the RBR technology. The prototype proved that a mobile reactor can greatly reduce the process time for larger water volumes compared to a stationary RBR. The aim of this thesis is to develop the next version of the mobile reactor, with increased operational stability and autonomous driving (autopilot) as main goals. This work covers all parts in the development of the new mobile reactor which involves design, simulation, construction, electronics, software implementations and testing. The presented mobile reactor is a twin hull surface vehicle with the possibility of using two RBRs for water treatment. The steering is based on differential motor thrust and the autonomous driving was achieved using sensor data from a GPS, magnetometer and accelerometer, together with a proportional-integral-derivative (PID) type control system. The autopilot was put to the test on two different travel routes with a P and PI controller. The mobile reactor successfully followed the given routes, thus verifying that the developed mobile reactor can be used for future autonomous large scale water treatment.  

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  • 45.
    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.

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    Wave study - Seaflex AB
  • 46.
    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.

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  • 47.
    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.

  • 48. Bernardo-Madrid, Rubén
    et al.
    Calatayud, Joaquín
    Umeå University, Faculty of Science and Technology, Department of Physics. Department of Life Science, Universidad de Alcalá, Alcalá de Henares, Spain; Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.
    González-Suárez, Manuela
    Rosvall, Martin
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lucas, Pablo M.
    Rueda, Marta
    Antonelli, Alexandre
    Revilla, Eloy
    Human activity is altering the world's zoogeographical regions2019In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 22, no 8, p. 1297-1305Article in journal (Refereed)
    Abstract [en]

    Zoogeographical regions, or zooregions, are areas of the Earth defined by species pools that reflect ecological, historical and evolutionary processes acting over millions of years. Consequently, researchers have assumed that zooregions are robust and unlikely to change on a human timescale. However, the increasing number of human‐mediated introductions and extinctions can challenge this assumption. By delineating zooregions with a network‐based algorithm, here we show that introductions and extinctions are altering the zooregions we know today. Introductions are homogenising the Eurasian and African mammal zooregions and also triggering less intuitive effects in birds and amphibians, such as dividing and redefining zooregions representing the Old and New World. Furthermore, these Old and New World amphibian zooregions are no longer detected when considering introductions plus extinctions of the most threatened species. Our findings highlight the profound and far‐reaching impact of human activity and call for identifying and protecting the uniqueness of biotic assemblages.

  • 49.
    Bernenko, Dolores
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Exploring the multiscale 3D architecture of human chromosome contact networks2023Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Cells regulate genes to coordinate essential functions allowing cells to grow, divide, specialize, and respond to stresses. While regulatory proteins are the most common way to control these genes, the DNA’s 3D structure also plays a critical role as it affects how proteins access genes and how regulatory DNA elements interact over large genomic distances. This thesis explores the latter aspect of gene regulation by mapping DNA’s 3D multiscale architecture and exploring the within-scale variability.

    To study these aspects, we analyzed empirical DNA-DNA contact data from a technique known as Hi-C. This technique measures the contact frequency between pairs of points on DNA. To infer multiscale DNA 3D structures from this data set, we adopt and develop a community detection framework that finds the groups of interconnected DNA regions. Rooted in network science, this approach allowed us to study the DNA’s ensemble-averaged 3D organization while embracing its complexity and variability.

    In this work, we mapped DNA’s multiscale 3D architecture and demonstrated how our community detection algorithm charts the structural scales in regimes that are often opaque to other computational tools. We also addressed several specific research questions. First, we explored cross-scale 3D structures, quantifying to what extent their interactions are hierarchical. We also determined the scales where the 3D structures seem most robust and quantified the DNA's structural ambiguities. Additionally, we explored the association between DNA's 3D architecture and epigenetic states. Finally, we demonstrated how our framework applies to another DNA contact data set (HiChIP) that may be useful to better understand spatial rearrangements in cancer cells. 

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  • 50.
    Bernenko, Dolores
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Lee, Sang Hoon
    Department of Physics and Research Institute of Natural Science, Gyeongsang National University, Jinju, Republic of Korea; Future Convergence Technology Research Institute, Gyeongsang National University, Jinju, Republic of Korea.
    Lizana, Ludvig
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Exploring 3D community inconsistency in human chromosome contact networks2023In: Journal of physics. Complexity, ISSN 2632-072X, Vol. 4, no 3, article id 035004Article in journal (Other academic)
    Abstract [en]

    Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is common to group these pairs using standard bioinformatics methods (e.g., PCA). Other approaches handle Hi-C data as weighted networks, where connected node represent DNA segments in 3D proximity. In this representation, one can leverage community detection techniques developed in complex network theory to group nodes into mesoscale communities containing similar connection patterns. While there are several successful attempts to analyze Hi-C data in this way, it is common to report and study the most typical community structure. But in reality, there are often several valid candidates. Therefore, depending on algorithm design, different community detection methods focusing on slightly different connectivity features may have differing views on the ideal node groupings. In fact, even the same community detection method may yield different results if using a stochastic algorithm. This ambiguity is fundamental to community detection and shared by most complex networks whenever interactions span all scales in the network. This is known as community inconsistency. This paper explores this inconsistency of 3D communities in Hi-C data for all human chromosomes. We base our analysis on two inconsistency metrics, one local and one global, and quantify the network scales where the community separation is most variable. For example, we find that TADs are less reliable than A/B compartments and that nodes with highly variable node-community memberships are associated with open chromatin. Overall, our study provides a helpful framework for data-driven researchers and increases awareness of some inherent challenges when clustering Hi-C data into 3D communities.

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