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  • Public defence: 2025-02-10 09:15 Polhem, Uppsala
    Salar, Dana
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Electrical Engineering, Electricity.
    Industrial robot as main equipment for testing and production of Wave Energy Converters2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since 2001, research and development on the conversion of ocean wave energy into electricity has been conducted at the Division of Electricity at Uppsala University. Different Wave Energy Converter (WEC) technologies has been developed, such as the point-absorber linear Uppsala University WEC (UU-WEC) and the Low-RPM Torque Converter WEC (LRTC-WEC). 

    This thesis focuses primarily on the development of a robotized dry test rig, to facilitate assessment of different WEC technologies in house. An existing industrial six degrees of freedom robot system is used to emulate buoy movement on the sea surface, with regard to the impact of hydrodynamic forces in real time. Two different methods for integrating a hydrodynamic model to the robot controller are presented: the force control and the position control methods. Both methods are evaluated and validated across various regular and irregular wave climates, as well as for different theoretical buoy shapes.  

    The secondary focus in this thesis is the development of robotized production methods for the UU-WEC. The surface mounting of Neodymium Iron Boron (Nd2Fe14B) magnets and the cutting of rubber discs are investigated, resulting in viable solutions that include development and validation of robot tooling and robot cell proposals. 

    A smaller segment of the thesis examines the use of robotics in teaching a course for bachelor engineering students. At the outbreak of the COVID-19 pandemic a challenging task was imposed: a swift shift to online distant education. A major task was to replace physical lab exercises with video recordings, detailed instructions and simulated laboratory environments. The results indicated that the upgraded online education successfully meet the course objectives.

    The final part of the thesis investigates the use of WECs for powering a desalination plant. Desalination presents a viable solution for islands or coastal regions deficient in freshwater resources, but is also an energy intensive process. Practical experiment evaluated the possibility of utilizing the UU-WEC as power source for desalination plants.

    List of papers
    1. Preparing the Uppsala University wave energy converter generator for large-scale production
    Open this publication in new window or tab >>Preparing the Uppsala University wave energy converter generator for large-scale production
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    2014 (English)Conference paper, Published paper (Other academic)
    Place, publisher, year, edition, pages
    Halifax, Canada: , 2014
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-237554 (URN)
    Conference
    5th International Conference on Ocean Energy
    Available from: 2014-12-03 Created: 2014-12-03 Last updated: 2024-12-10
    2. Learnings from the rapid online transition of a real-world project task-based engineering course
    Open this publication in new window or tab >>Learnings from the rapid online transition of a real-world project task-based engineering course
    2022 (English)In: 2022 IEEE Frontiers in Education Conference (FIE), Institute of Electrical and Electronics Engineers (IEEE), 2022Conference paper, Published paper (Refereed)
    Abstract [en]

    This Innovative Practice Full Paper presents the results and learnings from a rapid and forced transition to online teaching of a campus-based and practical lab exercise intense course in robot engineering. Founded in previous pedagogical development work, we continued with activating and varied teaching methods connected through integrated project tasks. The online transition is evaluated from student course evaluations, examination results and the teachers’ experiences from ten campus course occasions and four online course occasions during ten years. The paper focuses specifically on the combination of an innovative online lecturing format and fully virtual robot lab exercises. Our aim is to present learnings of interest for the engineering education community. The results highlight a successful and appreciated online course transition, with possibly improved student learning. In particular the prerecorded video lectures were praised, the virtual labs was similarly appreciated as campus labs and it was demonstrated that online robot programming can be performed virtually, while practical lab exercises and study visits were still missed.

    Place, publisher, year, edition, pages
    Institute of Electrical and Electronics Engineers (IEEE), 2022
    Series
    IEEE Frontiers in Education Conference, ISSN 1539-4565, E-ISSN 2377-634X
    Keywords
    engineering education, project organized learning, online teaching, virtual lab exercises, video lectures
    National Category
    Didactics Robotics and automation
    Identifiers
    urn:nbn:se:uu:diva-489940 (URN)10.1109/FIE56618.2022.9962454 (DOI)001204427600080 ()2-s2.0-85143810738 (Scopus ID)978-1-6654-6245-7 (ISBN)978-1-6654-6244-0 (ISBN)
    Conference
    IEEE Frontiers in Education Conference, FIE 2022, Uppsala, Sweden, October 8-11, 2022
    Funder
    Uppsala University
    Available from: 2022-12-06 Created: 2022-12-06 Last updated: 2025-02-05Bibliographically approved
    3. A robotized 6-DOF dry test rig for wave power
    Open this publication in new window or tab >>A robotized 6-DOF dry test rig for wave power
    2023 (English)In: Sustainable Energy Technologies and Assessments, ISSN 2213-1388, E-ISSN 2213-1396, Vol. 59, article id 103393Article in journal (Refereed) Published
    Abstract [en]

    Wave power has the potential to contribute significantly to sustainability by reducing our global dependence on fossil fuels. Due to harsh conditions and high costs associated with offshore testing, lab experiments are favourable for resource-efficient validation and optimization in developing Wave Energy Converter (WEC) technologies. The limited scale and availability of existing wave tanks, and the limited flexibility of existing dry test rigs does however put significant restraints on such experiments. In this paper we introduce an alternative novel robotized dry test rig concept for wave power, evaluate its performance and discuss its potential. A full-scale robotized dry test rig demonstrator is constructed and used for experiments with a WEC prototype device. High motion flexibility and accuracy is thereby validated, also for repeating recorded wave and buoy motions. Compared to other dry test rigs, no special components were used and the motion trajectories were defined in full 6-Degrees-Of-Freedom. Two real-time hydrodynamic motion response methods are also demonstrated in the test rig, enabling emulation of actual offshore operation as well as development of advanced WEC control strategies. With a larger industrial robot manipulator, the introduced test rig concept could achieve realistic scaled force and power experiments with most point absorber WECs.

    Place, publisher, year, edition, pages
    Elsevier, 2023
    Keywords
    Dry test rig, Wave emulator, Industrial robot, Wave energy converter, Renewable energy
    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-509121 (URN)10.1016/j.seta.2023.103393 (DOI)001124250700001 ()
    Available from: 2023-08-15 Created: 2023-08-15 Last updated: 2024-12-10Bibliographically approved
    4. Robotized manufacturing of rubber components for commercialization of the Uppsala University wave energy converter concept
    Open this publication in new window or tab >>Robotized manufacturing of rubber components for commercialization of the Uppsala University wave energy converter concept
    2016 (English)Conference paper, Published paper (Other academic)
    Place, publisher, year, edition, pages
    Glasgow, UK: , 2016
    National Category
    Engineering and Technology
    Identifiers
    urn:nbn:se:uu:diva-334547 (URN)
    Conference
    2nd International Conference on Offshore Renewable Energy
    Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2024-12-10
    5. Robotized Surface Mounting of Permanent Magnets
    Open this publication in new window or tab >>Robotized Surface Mounting of Permanent Magnets
    2014 (English)In: Machines, Vol. 2, no 4, p. 219-232Article in journal (Refereed) Published
    Abstract [en]

    Using permanent magnets on a rotor can both simplify the design and increase the efficiency of electric machines compared to using electromagnets. A drawback, however, is the lack of existing automated assembly methods for large machines. This paper presents and motivates a method for robotized surface mounting of permanent magnets on electric machine rotors. The translator of the Uppsala University Wave Energy Converter generator is used as an example of a rotor. The robot cell layout, equipment design and assembly process are presented and validated through computer simulations and experiments with prototype equipment. A comparison with manual assembly indicates substantial cost savings and an improved work environment. By using the flexibility of industrial robots and a scalable equipment design, it is possible for this assembly method to be adjusted for other rotor geometries and sizes. Finally, there is a discussion on the work that remains to be done on improving and integrating the robot cell into a production line.

    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-237449 (URN)10.3390/machines2040219 (DOI)
    Available from: 2014-12-02 Created: 2014-12-02 Last updated: 2024-12-10
    6. Variable renewable energy sources for powering reverse osmosis desalination, with a case study of wave powered desalination for Kilifi, Kenya
    Open this publication in new window or tab >>Variable renewable energy sources for powering reverse osmosis desalination, with a case study of wave powered desalination for Kilifi, Kenya
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    2020 (English)In: Desalination, ISSN 0011-9164, E-ISSN 1873-4464, Vol. 494, no 114669Article in journal (Refereed) Published
    Abstract [en]

    An analysis of reverse osmosis powered by ocean wave power is provided. A commercially available desalination system is connected via a DC/AC converter to a variable DC source and the input voltage is altered to emulate the response of a renewable energy system. Specifically, wave data from Kilifi in Kenya during 2015 is used. The wave resource variations provide variations in estimated power output from a wave energy converter, as well as in estimated freshwater production from a wave powered desalination system. Up to three wave energy converters for desalination are investigated for Kilifi. Also, a hybrid system including solar and wave power is proposed. The experiments show that reverse osmosis desalination systems can function at power levels below the rated values, but with lower freshwater flowrates. It is concluded that wave power, or wave power combined with PV systems, may be considered as power sources for desalination, with or without battery storage.

    Place, publisher, year, edition, pages
    Elsevier BV, 2020
    Keywords
    Reverse osmosis desalination, Ocean wave power, Renewable energy sources, Freshwater, Vågkraft, avsaltning
    National Category
    Other Electrical Engineering, Electronic Engineering, Information Engineering
    Research subject
    Engineering Science with specialization in Science of Electricity
    Identifiers
    urn:nbn:se:uu:diva-417909 (URN)10.1016/j.desal.2020.114669 (DOI)000571849600003 ()
    Funder
    Swedish Research CouncilStandUp
    Available from: 2020-08-27 Created: 2020-08-27 Last updated: 2024-12-10Bibliographically approved
    7. Emulating Wave Energy Converter operation in irregular waves using a robotized dry test rig
    Open this publication in new window or tab >>Emulating Wave Energy Converter operation in irregular waves using a robotized dry test rig
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Wave Energy Converter (WEC) technology has for a long time captured the interest of researchers, in the strive to increase and diversify the share of renewables in our global energy system. The development of WECs is however challenging due to the time-consuming and expensive open sea experiments required. Controlled wave tank testing is therefore often used, but suffer from the limited availability, scale and wave conditions that can be achieved. Another option is dry test rigs, utilizing a mechanical actuator to emulate WEC operation in ocean waves. Achieving realistic tests is however a challenge.

    This work focuses on a robotized dry test rig, providing a cost-effective, industrial and flexible test concept for one-body and two-body emulation of point-absorber WECs in in all six degree of freedom. A numerical linear potential flow hydrodynamic force model for simulating the motions in irregular waves is presented and evaluated against wave tank experiments, before being implemented on the robot controller. Test rig experiments based on a simulated WEC damping force and assuming a one-body system acting purely in heave are presented.

    We successfully demonstrated WEC operation emulation in irregular waves with the robot test rig, and were also able to evaluate its accuracy. It can be concluded that the robot performs well in relation to the numerical model, while the numerical model performs satisfying mainly for smaller and non-steep waves. Further work is therefore suggested on expanding the emulation to several degrees of freedom and also to include a physical WEC power take-off unit.

    Keywords
    Dry test rig, Industrial robot, Wave Energy Converter, Hydrodynamic modelling, Irregular waves
    National Category
    Robotics
    Research subject
    Engineering science with specialization in Applied Mechanics; Engineering Science with specialization in industrial engineering and management
    Identifiers
    urn:nbn:se:uu:diva-544284 (URN)
    Note

    Artikeln har inlämnats/submitted

    Available from: 2024-12-03 Created: 2024-12-03 Last updated: 2025-02-05
    8. Demonstrating real-time hydrodynamic motion response in force control for regular waves in a robotized dry test rig with a point-absorber WEC
    Open this publication in new window or tab >>Demonstrating real-time hydrodynamic motion response in force control for regular waves in a robotized dry test rig with a point-absorber WEC
    2023 (English)In: Proceedings of the 15th European Wave and Tidal Energy Conference, Bilbao, 3-7 September 2023. / [ed] Jesús María Blanco Ilzarbe, Bilbao: European Wave and Tidal Energy Conference , 2023, Vol. 15Conference paper, Published paper (Refereed)
    Abstract [en]

    A 6-Degrees-Of-Freedom robotized dry test rig has been developed at Uppsala University to test point absorbing WECs (Wave Energy Converters). Using a six joint industrial robot as a buoy movement emulator, the robot's outermost point (joint 6) is connected to the wire from the generator concept WEC PTO (Power Take-Off). The robot's movement in joint 6 thus corresponds to the buoy movement on the sea surface. The test rig can be used for various point absorbing WEC PTO units. In this project, the test rig has been used with a WEC-PTO prototype. The point absorbing WEC-LRTC concept is being developed at Uppsala University. The generator concept is made up of two identical rotating generators. A wire is used as a connection between the generator concept at the seabed and a buoy on the sea surface.  The goal of this article is to demonstrate and evaluate how the test rig interacts with the LRTC-WEC PTO in regular waves. In the presented experiments, a hydrodynamic model with force control method has been used.  The results show a clear difference in the use of the hydrodynamic model with different sizes of the buoy. The test rig with the force control model can be used easily to test different theoretical buoys and different load settings for WEC PTOs. Effective experiments can be performed with real PTO forces instead of simplified simulations.  Future work is to experiment with the position control method and also experiments with irregular waves.

    Place, publisher, year, edition, pages
    Bilbao: European Wave and Tidal Energy Conference, 2023
    Keywords
    LRTC, point-absorber, dry test rig, wave emulator, industrial robot, wave energy converter
    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-518384 (URN)10.36688/ewtec-2023-643 (DOI)
    Conference
    15th European Wave and Tidal Energy Conference (EWTEC)
    Available from: 2023-12-18 Created: 2023-12-18 Last updated: 2024-12-10Bibliographically approved
    9. Evaluating position control for real-time hydrodynamic motion response in a robotized dry test rig with a point-absorber wave energy converter
    Open this publication in new window or tab >>Evaluating position control for real-time hydrodynamic motion response in a robotized dry test rig with a point-absorber wave energy converter
    2024 (English)In: Proceedings of the ASME 2024 43rd International Conference on Ocean, Offshore and Arctic Engineering: Volume 1: Offshore Technology, Singapore, 2024, Vol. 1Conference paper, Published paper (Refereed)
    Abstract [en]

    A robotized dry test rig in six degrees of freedom, for emulating the influence of hydrodynamic forces on and the resulting motion response of different types of point absorbing wave energy converters has been developed at Uppsala University. In the past we have investigated and shown that the dry test rig works with both force and position control methods.In this article we further examine the position control method, as we have not been able to use it for rougher wave movements. This is due to the fact that there has been a control lag in the system which contributed to the system becoming unbalanced in some emulation scenarios. A solution for an updated position control method, with significantly reduced control lag, is demonstrated in robot simulations and compared with both hydrodynamic model simulations and physical robot experiments for two buoy sizes in regular waves.

    The results show a clear positive solution for avoiding control lag problems, making the position control method fully possible to use in the field. Future work is to implement the updated method on the physical robot test rig.

    Place, publisher, year, edition, pages
    Singapore: , 2024
    Keywords
    dry test rig, industrial robot, point-absorber, wave emulator, wave energy converter
    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-540698 (URN)10.1115/OMAE2024-121981 (DOI)
    Conference
    ASME 2024 43rd International Conference on Ocean, Offshore and Arctic Engineering
    Available from: 2024-10-18 Created: 2024-10-18 Last updated: 2024-12-10
    10. Low-RPM torque converter (LRTC) with Integrated direct shaft flywheel
    Open this publication in new window or tab >>Low-RPM torque converter (LRTC) with Integrated direct shaft flywheel
    2023 (English)In: International Marine Energy Journal, E-ISSN 2631-5548, Vol. 6, no 1, p. 1-10Article in journal (Refereed) Published
    Abstract [en]

    The low-RPM Torque Converter (LRTC) is a rotating generator concept for use on the seabed with the driving force from sea waves motion on the sea surface. This concept is built up of two identical generators connected opposite each other via a spring drum with a built-in ball bearing clutch. The drum is connected to a buoy on the sea surface via a wire, the wire is rolled around the spring drum. With sea waves, the buoy moves either upwards or downwards and pulls the wire upwards or downwards. This movement causes the generators to spin.

    This article presents an upgrade of the LRTC generator concept and upgraded measurement system, both hardware and software.

    A flywheel system of the thin-disc type has been designed for direct connection to the generator's rotor shaft and an electronic measuring system has also been developed for more accurate measurements and minor disturbances.

    More detailed tests have been performed both for the purpose of comparing the systems and to explore the performance of the generator concept in more detail.

    Three different experiments have been done in this article. The first two experiments were performed to investigate the performance of the flywheel and to see the performance of the LRTC system with and without flywheel.

    The third experiment investigated the optimization of the flywheel mass by increasing the mass of the flywheel with the addition of more thin discs.

    All movements are simulated with a six-joint industrial robot. Several sinusoidal types of wave motions have been simulated with different time periods and also several real wave climate motions (data taken from fields) have been simulated with the robot. The experiments show that the addition of the flywheel in the LRTC system provides advantages in increasing both peak power, average output power and also softens the output power oscillation.

    Keywords
    LRTC; Flywheel; Robot; Generator; Wave energy; Renewable energy
    National Category
    Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:uu:diva-501121 (URN)10.36688/imej.6.1-10 (DOI)
    Available from: 2023-05-02 Created: 2023-05-02 Last updated: 2024-12-10
    11. Low-RPM Torque Converter (LRTC)
    Open this publication in new window or tab >>Low-RPM Torque Converter (LRTC)
    2021 (English)In: Energies, E-ISSN 1996-1073, Vol. 14, no 16, article id 5071Article in journal (Refereed) Published
    Abstract [en]

    The concept concerned in this paper is based on energy conversion of the ocean waves via rotational generators. The objective of this research is to develop a new type of slow-motion converter. The LRTC device consists of a drum that is connected via wire to a floating buoy. The drum is connected to rotary generators. The generators are heavily braked when the direction of movement changes (up/down); this is because the generators have been charged the maximum load in order to obtain maximum output power. For upcoming improvement, the generators should have some power storage as flywheel. In the future experiments, the torque converter can even be tuned to rotate in resonance with the incoming waves, strongly increasing power absorption. Constant force springs are applied for this purpose. The focus of this project is, therefore, a new generation of wave power device for utility-scale energy conversion offering a cost of energy that can compete with established energy resources.

    Place, publisher, year, edition, pages
    MDPIMDPI AG, 2021
    Keywords
    wave energy conversion, torque converter, resonance frequency
    National Category
    Other Electrical Engineering, Electronic Engineering, Information Engineering Energy Engineering
    Identifiers
    urn:nbn:se:uu:diva-455502 (URN)10.3390/en14165071 (DOI)000690643600001 ()
    Funder
    StandUp
    Available from: 2021-10-07 Created: 2021-10-07 Last updated: 2024-12-10Bibliographically approved
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  • Public defence: 2025-02-11 09:15 Å101121, Sonja-Lyttkens, Ångströmlaboratoriet, Uppsala
    Knijff, Lisanne
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Dipole and Charge Prediction for Electrochemical Systems from Atomistic Machine Learning2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Due to the increasing demand for energy, sustainable energy generation and storage are becoming more and more important in society and research. Electrochemical energy storage devices such as electrochemical double-layer capacitors (EDLCs) play an important role in fulfilling this need. To understand, control and design EDLCs at atomic precision, physical insights from atomistic simulation are clearly needed. However, atomistic simulation of EDLCs faces challenges such as the large system size and the complex chemistry involved at electrified solid-liquid interfaces. To address these challenges, machine learning models for charge prediction have been developed to aid the atomistic simulations of EDLCs in this thesis. Here, a divide-and-conquer approach was taken, and the electrolyte and electrode component were investigated separately.

    Initially, a neural network approach called PiNet-dipole was developed to model the supercell polarization in liquid water using two constraints. First, the displacement of the atomic charges is proportional to the itinerant polarization. Second, each water molecule has a net charge of zero. In doing so, a molecular dipole moment distribution can be inferred for liquid water that is surprisingly similar to that computed from Wannier centers. More importantly, PiNet-dipole provides a way to predict atomic charge without resorting to any predefined charge partition schemes. This is followed by using a class of machine learning models called PiNet-chi to predict the response charge as the result of an applied electric field for both organic electrolyte molecules and graphene analogues. Both of these models were then upgraded through the addition of equivariant features in PiNet2. This opened up new ways of predicting dipole moment for both small molecules and condensed phase systems, allowing expansion to the PiNet2-dipole family and enabling a more expressive atomic charge prediction model.

    Finally, by combining the PiNet(2)-dipole and the PiNet(2)-chi models and integrating them with the semi-classical molecular dynamics code MetalWalls, the PiNNwall interface was developed to model polarizable and heterogeneous electrodes. PiNNwall was then used to study chemically doped graphene and graphene oxide under different electrical boundary conditions, as well as to investigate the influence of the proton charge on aqueous EDLCs.

    List of papers
    1. Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes
    Open this publication in new window or tab >>Modeling of Nanomaterials for Supercapacitors: Beyond Carbon Electrodes
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    2024 (English)In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 18, no 31, p. 19931-19949Article, review/survey (Refereed) Published
    Abstract [en]

    Capacitive storage devices allow for fast charge and discharge cycles, making them the perfect complements to batteries for high power applications. Many materials display interesting capacitive properties when they are put in contact with ionic solutions despite their very different structures and (surface) reactivity. Among them, nanocarbons are the most important for practical applications, but many nanomaterials have recently emerged, such as conductive metal-organic frameworks, 2D materials, and a wide variety of metal oxides. These heterogeneous and complex electrode materials are difficult to model with conventional approaches. However, the development of computational methods, the incorporation of machine learning techniques, and the increasing power in high performance computing now allow us to tackle these types of systems. In this Review, we summarize the current efforts in this direction. We show that depending on the nature of the materials and of the charging mechanisms, different methods, or combinations of them, can provide desirable atomic-scale insight on the interactions at play. We mainly focus on two important aspects: (i) the study of ion adsorption in complex nanoporous materials, which require the extension of constant potential molecular dynamics to multicomponent systems, and (ii) the characterization of Faradaic processes in pseudocapacitors, that involves the use of electronic structure-based methods. We also discuss how recently developed simulation methods will allow bridges to be made between double-layer capacitors and pseudocapacitors for future high power electricity storage devices.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2024
    Keywords
    Pseudocapacitors, Doublelayer, MXene, Metal-organic framework, 2D materials, Metaloxides, Molecular dynamics, Machine-learning
    National Category
    Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-544551 (URN)10.1021/acsnano.4c01787 (DOI)001279682400001 ()39053903 (PubMedID)2-s2.0-85199565614 (Scopus ID)
    Funder
    EU, Horizon 2020, 945298EU, Horizon 2020, 949012Uppsala UniversityKnut and Alice Wallenberg Foundation
    Available from: 2024-12-05 Created: 2024-12-05 Last updated: 2024-12-10Bibliographically approved
    2. Machine learning inference of molecular dipole moment in liquid water
    Open this publication in new window or tab >>Machine learning inference of molecular dipole moment in liquid water
    2021 (English)In: Machine Learning: Science and Technology, E-ISSN 2632-2153, Vol. 2, no 3, article id 03LT03Article in journal (Refereed) Published
    Abstract [en]

    Molecular dipole moment in liquid water is an intriguing property, partly due to the fact that there is no unique way to partition the total electron density into individual molecular contributions. The prevailing method to circumvent this problem is to use maximally localized Wannier functions, which perform a unitary transformation of the occupied molecular orbitals by minimizing the spread function of Boys. Here we revisit this problem using a data-driven approach satisfying two physical constraints, namely: (a) The displacement of the atomic charges is proportional to the Berry phase polarization; (b) Each water molecule has a formal charge of zero. It turns out that the distribution of molecular dipole moments in liquid water inferred from latent variables is surprisingly similar to that obtained from maximally localized Wannier functions. Apart from putting a maximum-likelihood footnote to the established method, this work highlights the capability of graph convolution based charge models and the importance of physical constraints on improving the model interpretability.

    National Category
    Theoretical Chemistry Physical Chemistry Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-464076 (URN)10.1088/2632-2153/ac0123 (DOI)
    Funder
    EU, Horizon 2020, 949012
    Available from: 2022-01-13 Created: 2022-01-13 Last updated: 2024-12-09Bibliographically approved
    3. Finite-field coupling via learning the charge response kernel
    Open this publication in new window or tab >>Finite-field coupling via learning the charge response kernel
    2022 (English)In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 1, article id 014012Article in journal (Refereed) Published
    Abstract [en]

    Response of the electronic density at the electrode–electrolyte interface to the external field (potential) is fundamental in electrochemistry. In density-functional theory, this is captured by the so-called charge response kernel (CRK). Projecting the CRK to its atom-condensed form is an essential step for obtaining the response charge of atoms. In this work, the atom-condensed CRK is learnt from the molecular polarizability using machine learning (ML) models and subsequently used for the response-charge prediction under an external field (potential). As the machine-learnt CRK shows a physical scaling of polarizability over the molecular size and does not (necessarily) require the matrix-inversion operation in practice, this opens up a viable and efficient route for introducing finite-field coupling in the atomistic simulation of electrochemical systems powered by ML models.

    Place, publisher, year, edition, pages
    Institute of Physics Publishing (IOPP), 2022
    National Category
    Theoretical Chemistry
    Research subject
    Chemistry with specialization in Physical Chemistry; Chemistry with Specialisation in Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-481503 (URN)10.1088/2516-1075/ac59ca (DOI)000897703700001 ()
    Funder
    EU, Horizon 2020, 949012
    Available from: 2022-08-11 Created: 2022-08-11 Last updated: 2024-12-09Bibliographically approved
    4. PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation
    Open this publication in new window or tab >>PiNNwall: Heterogeneous Electrode Models from Integrating Machine Learning and Atomistic Simulation
    2023 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 15, p. 5199-5209Article in journal (Refereed) Published
    Abstract [en]

    Electrochemical energy storage always involves the capacitive process. The prevailing electrode model used in the molecular simulation of polarizable electrode–electrolyte systems is the Siepmann–Sprik model developed for perfect metal electrodes. This model has been recently extended to study the metallicity in the electrode by including the Thomas–Fermi screening length. Nevertheless, a further extension to heterogeneous electrode models requires introducing chemical specificity, which does not have any analytical recipes. Here, we address this challenge by integrating the atomistic machine learning code (PiNN) for generating the base charge and response kernel and the classical molecular dynamics code (MetalWalls) dedicated to the modeling of electrochemical systems, and this leads to the development of the PiNNwall interface. Apart from the cases of chemically doped graphene and graphene oxide electrodes as shown in this study, the PiNNwall interface also allows us to probe polarized oxide surfaces in which both the proton charge and the electronic charge can coexist. Therefore, this work opens the door for modeling heterogeneous and complex electrode materials often found in energy storage systems.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2023
    National Category
    Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-510937 (URN)10.1021/acs.jctc.3c00359 (DOI)001033844500001 ()37477645 (PubMedID)
    Funder
    EU, Horizon 2020, 949012Swedish Research Council, 2022-06725
    Available from: 2023-09-13 Created: 2023-09-13 Last updated: 2024-12-09Bibliographically approved
    5. PiNN: equivariant neural network suite for modelling electrochemical systems
    Open this publication in new window or tab >>PiNN: equivariant neural network suite for modelling electrochemical systems
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    2024 (English)In: Article in journal (Other academic) Submitted
    Abstract [en]

    Electrochemical energy storage and conversion play an increasingly important role in electrification and sustainable development across the globe. A key challenge therein is to understand, control, and design electrochemical energy materials at atomistic precision. This requires inputs from molecular modelling powered by machine learning (ML) techniques. In this work, we have upgraded our pairwise interaction neural network Python package PiNN via introducing equivariant features to the PiNet2 architecture for fitting potential energy surfaces along with PiNet2-dipole for dipole and charge predictions as well as PiNet2-chi for generating atom-condensed charge response kernels. By benchmarking publicly accessible datasets of small molecules, crystalline materials, and liquid electrolytes, we found that the equivariant PiNet2 shows significant improvements over the original PiNet architecture and provides a state-of-the-art overall performance. Furthermore, leveraging on plug-ins such as PiNNAcLe for an adaptive learn-on-the-fly workflow in generating ML potentials and PiNNwall for modelling heterogeneous electrodes under external bias, we expect PiNN to serve as a versatile and high-performing ML-accelerated platform for molecular modelling of electrochemical systems.

    Keywords
    machine learning, molecular dynamics, liquid electrolyte, ion transport, proton transfer, double layer, supercapacitor
    National Category
    Computer and Information Sciences Materials Chemistry
    Research subject
    Chemistry with specialization in Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-544807 (URN)10.26434/chemrxiv-2024-zfvrz (DOI)
    Funder
    EU, European Research Council, 949012Knut and Alice Wallenberg Foundation, WISE-AP01- PD37
    Note

    The first two authors share first authorship.

    Available from: 2024-12-09 Created: 2024-12-09 Last updated: 2024-12-09
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  • Public defence: 2025-02-14 09:00 Krakow
    Sordyl, Julia
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Mineralogy Petrology and Tectonics. AGH University of Krakow, Faculty of Geology, Geophysics and Environmental Protection.
    Experimental immobilization of REE, Th and U by precipitation of pyromorphite [Pb5(PO4)3Cl]2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The globally increasing demand for rare earth elements (REE) opens up a vast field for the exploration of new methods for recovery of these metals from various sources. Extensive Research & Development is being conducted for each of the processing steps, i.e. (1) REE leaching, (2) REE immobilization, and (3) separation of individual REE as well as the accompanying thorium (Th) and uranium (U). Innovative and sustainable ideas for each of the steps are necessary to effectively face the global challenge of the continuous supply of these valuable metals.

    This thesis seeks to explore new method of recovering REE, Th and U from solutions. The basic idea was that precipitation of pyromorphite [Pb5(PO4)3Cl] could efficiently removes metals from solution and immobilize them in a stable, crystalline phase. The main objectives were to quantify the REE, Th and U removal from aqueous solutions upon precipitation of pyromorphite and to determine the structural position of incorporated metals in its structure. Controlled laboratory experiments were followed by quantitative analyses of solutions and characterization of solids.

    The results confirmed that pyromorphite precipitation under ambient conditions is an effective (>99%) method for removing REE, Th and U(VI) from solutions. Initial Pb concentration and pH of the synthesis affect the form of the resulting precipitate. There are no differences in the level of removal from solution of individual lanthanides. The latter preferentially substitute in the pyromorphite structure at the M1 position together with charge-balancing ions. In contrast, due to charge differences, U(VI) substitutes for Pb on the basis of the following substitution: (UO2)2+ ↔ Pb2+. Scandium and thorium tend to form a separate phase(s), but their removability from solution is equally high.

    Altogether, in the scope of this thesis, a promising method for efficient recovery of REE from solutions was discovered and tested in laboratory scale. Moreover, the substitutions of REE, Th and U(VI) in pyromorphite, a member of the apatite supergroup, have not previously been studied in depth. Therefore, this research and the obtained results have contributed to fill this gap in the context of widely reported mineralogical and structural studies of apatite supergroup members. 

    List of papers
    1. Removal of REE and Th from solution by co-precipitation with Pb-phosphates
    Open this publication in new window or tab >>Removal of REE and Th from solution by co-precipitation with Pb-phosphates
    2023 (English)In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 158, article id 105780Article in journal (Refereed) Published
    Abstract [en]

    The supply of technologically important rare earth elements (REE) is a concern in Europe, hence the recovery of REE from alternative sources has recently become widely investigated. One of the problems is the lack of cost-effective technologies for REE recovery from leaching solutions. The present work investigated the potential for recovering REE and Th from leaching solutions by co-precipitation with Pb phosphates. A set of four experiments were conducted using analytical reagent grade chemicals to analyze the effects of Pb and different pH on the efficiency of REE and Th removal from aqueous solutions. After selecting the best conditions, two additional experiments were performed using solutions obtained from leaching REE-rich apatite mine waste.The precipitates resulting from the experiments as well as the solutions before and after precipitation were analyzed. It was found that the formation of a crystalline mixture of REE-and Th-enriched pyromorphite, Pb-5(PO4)(3)Cl, and Pb-phosphates, about which little has been known so far, was responsible for complete (>99%) removal of REE and Th from aqueous solutions at pH 4 and 6. At lower pH, the removal is incomplete except for Sc and Th, which probably form a distinct phases. Besides that, no fractionation of LREE and HREE was observed. The experiments included the study of solutions resulting from the leaching of REE-rich apatite waste, which may contribute to the development of new technologies for REE recovery from wastes.

    Place, publisher, year, edition, pages
    ElsevierElsevier BV, 2023
    Keywords
    Rare earth elements, Recovery, Lanthanides, Pyromorphite
    National Category
    Geochemistry
    Identifiers
    urn:nbn:se:uu:diva-515313 (URN)10.1016/j.apgeochem.2023.105780 (DOI)001080856800001 ()
    Available from: 2023-11-03 Created: 2023-11-03 Last updated: 2025-01-10Bibliographically approved
    2. Single-crystal analysis of La-doped pyromorphite [Pb5(PO4)3Cl]
    Open this publication in new window or tab >>Single-crystal analysis of La-doped pyromorphite [Pb5(PO4)3Cl]
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    2023 (English)In: American Mineralogist, ISSN 0003-004X, E-ISSN 1945-3027, Vol. 108, no 12, p. 2323-2330Article in journal (Refereed) Published
    Abstract [en]

    Rare earth elements (REE) in calcium apatite have been widely described in the literature. Based on the investigations of minerals and their synthetic analogs, the mechanism of substitution of REE3+ for Ca2+ and their structural positions are well established. Although the presence of REE in natural pyromorphite has been reported, the structural response of substitution of REE3+ for Pb2+ is not established. A better understanding of REE-rich Pb-apatite may facilitate the potential use of this mineral in industrial processes. Two La-doped pyromorphite analogs [Pb5(PO4)3Cl] and two control pyromorphite analogs (with the absence of La) were synthesized from aqueous solutions at 25 degrees C. Na+ and K+ were used as charge-compensating ions to facilitate the incorporation of trivalent REE cations (La3+ + Na+ ↔ 2Pb2+ and La3+ + K+ ↔ 2Pb2+). Microprobe analysis, scanning electron microscopy, and Raman spectroscopy were used to confirm the purity of obtained phases. High-precision crystal structure refinements (R1 = 0.0140-0.0225) of all four compounds were performed from single-crystal X-ray diffraction data. The La content varied from 0.12(1) to 0.19(1) atoms per formula unit with the counter ions of K+ and Na+, respectively. Both substituting ions were accommodated at the Pb1 site only. By comparing the La-doped pyromorphite analogs with their control samples, it was possible to detect small changes in bond distances and polyhedral volumes caused by the La substitution. Variations in individual and mean interatomic distances reflected the cumulative effect of both the amount of substitution and ionic radii of substituting ions (La3+, Na+, and K+).

    Place, publisher, year, edition, pages
    Mineralogical Society of America, 2023
    Keywords
    Apatite, pyromorphite, crystal structure, rare earth elements
    National Category
    Inorganic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-527493 (URN)10.2138/am-2022-8664 (DOI)001197201200013 ()
    Available from: 2024-05-03 Created: 2024-05-03 Last updated: 2025-01-10Bibliographically approved
    3. Immobilization of uranium from aqueous solutions by room-temperature precipitation of pyromorphite [Pb5(PO4)3Cl]
    Open this publication in new window or tab >>Immobilization of uranium from aqueous solutions by room-temperature precipitation of pyromorphite [Pb5(PO4)3Cl]
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    2024 (English)In: Polyhedron, ISSN 0277-5387, E-ISSN 1873-3719, Vol. 252, article id 116891Article in journal (Refereed) Published
    Abstract [en]

    U(VI) in natural pyromorphite reaches 0.5 wt%. However, this depends on concentration of U in source solutions and the upper limit of incorporation of uranyl into pyromorphite at low temperature is unknown. If U(VI) incorporation capacity in the structure is high enough, Pb-apatite could be used in radioactive waste remediation. In this study, eight compounds were synthesized from aqueous solutions containing Pb2+, (UO2)2+, (PO4)3- and Cl- ions in a still water column under ambient conditions. In each synthesis, the molar ratio of (UO2)2+:Pb was varied, targeting composition Pb5-x(UO2)x(PO4)3Cl. The final solutions were analyzed with inductively coupled plasma optical emission spectroscopy (ICP-OES) for Pb and U(VI) concentrations, while dried solids were analyzed using powder X-ray diffraction (PXRD), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), wavelength dispersive X-ray spectroscopy (WDS) using an electron microprobe, and Raman spectroscopy. Synthesis products are synthetic analogs of pyromorphite containing (UO2)2+, partially substituting Pb2+. For the higher initial concentration of U, coprecipitation of a second phase/phases was observed. U was removed from the solution at levels ranging from 74.3 % (σ = 1.5) to 88 % (σ = 2), and Pb was removed at levels ranging from 91 % (σ = 2) to 96.8 % (σ = 1.9). Precipitation of pyromorphite from uranyl-contaminated solutions may immobilize uranyl in the form of highly insoluble, stable, crystalline Pb phosphates.

    Place, publisher, year, edition, pages
    Elsevier, 2024
    Keywords
    Removal, Incorporation, Synthetic, Apatite, Autunite
    National Category
    Inorganic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-527035 (URN)10.1016/j.poly.2024.116891 (DOI)001196724000001 ()
    Available from: 2024-04-26 Created: 2024-04-26 Last updated: 2025-01-10Bibliographically approved
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  • Public defence: 2025-02-14 09:15 B21, Uppsala
    Sánchez Fernández, Javier
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Model-based optimization of cancer immunotherapy combinations2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The use of cancer immunotherapies has transformed the treatment landscape for many cancer types. Unfortunately, not all patients respond to these therapies, and most of those who do eventually relapse. Combining cancer immunotherapies may improve patient outcomes. However, determining which molecules to combine, at which doses, and under which dosing schedules rarely is straightforward.

    Preclinical experiments offer the opportunity to test a wide variety of experimental conditions. This data, together with information about disease biology, can be integrated into a mathematical modeling framework, which can be used to simulate different scenarios, allowing researchers to prioritize the most promising drug combinations in the patient populations where the highest probability of success is expected. In a continuous cycle, the model can inform the design of novel biologic drugs with improved pharmacological properties to improve outcomes for a larger percentage of the patient population. This thesis aimed to develop modeling and simulation approaches to guide the development of cancer immunotherapy combinations by contributing to molecule design, preclinical experimental design, and translation of preclinical knowledge into clinical insights. 

    The translation of the preclinical tumor growth inhibition model suggested that identifying a clinical effect with CD3 T-cell bispecific antibodies in monotherapy may be challenging. However, combination with anti-PD-L1 is expected to more than double progression-free survival, duration of response and response rate, highlighting that combination approaches with these molecules need to be considered as early as possible. 

    Using preclinical data, a target engagement model for bispecific costimulators was developed that can be used to prospectively predict the clinical range of doses with maximum expected effect. Furthermore, the model allowed differentiating the contribution of drug exposure and target expression to drug pharmacology. Leveraging this model, the impact of binding affinity on drug pharmacology was explored in silico for nineteen different oncology indications. This identified a molecule with a 10-fold increase in binding affinity as a promising follow-up molecule that may lead to increased patient benefit, establishing a workflow that can combine preclinical data with clinical target expression to explore in silico optimized molecule designs. 

    Lastly, a novel semimechanistic model was developed to describe clinical pharmacokinetics of biologics under anti-drug antibody formation and associated loss of exposure. The model can be used to accurately establish clinical the dose-exposure-response relationship without excluding patients with loss of drug exposure, as well as to explore the relationship of patient covariates and dosing schedule on drug immunogenicity.  

    This work highlights how modeling and simulation can leverage preclinical data to answer key clinical questions, such as the expected clinical benefit of a drug combination, the optimal range of doses for molecules with complex exposure-response relationships, and the design of improved molecules. These approaches offer valuable tools for data-driven drug development.

    List of papers
    1. Preclinical InVivo Data Integrated in a Modeling Network Informs a Refined Clinical Strategy for a CD3 T-Cell Bispecific in Combination with Anti-PD-L1
    Open this publication in new window or tab >>Preclinical InVivo Data Integrated in a Modeling Network Informs a Refined Clinical Strategy for a CD3 T-Cell Bispecific in Combination with Anti-PD-L1
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    2022 (English)In: AAPS Journal, E-ISSN 1550-7416, Vol. 24, article id 106Article in journal (Refereed) Published
    Abstract [en]

    TYRP1-TCB is a CD3 T-cell bispecific (CD3-TCB) antibody for the treatment of advanced melanoma. A tumor growth inhibition (TGI) model was developed using mouse xenograft data with TYRP1-TCB monotherapy or TYRP1-TCB plus anti-PD-Ll combination. The model was translated to humans to inform a refined clinical strategy. From xenograft mouse data, we estimated an EC50 of 0.345 mg/L for TYRP1-TCB, close to what was observed in vitro using the same tumor cell line. The model showed that, though increasing the dose of TYRP1-TCB in monotherapy delays the time to tumor regrowth and promotes higher tumor cell killing, it also induces a faster rate of tumor regrowth. Combination with anti-PD-L1 extended the time to tumor regrowth by 25% while also decreasing the tumor regrowth rate by 69% compared to the same dose of TYRP1-TCB alone. The model translation to humans predicts that if patients' tumors were scanned every 6 weeks, only 46% of the monotherapy responders would be detected even at a TYRP1-TCB dose resulting in exposures above the EC90. However, combination of TYRP1-TCB and anti-PD-L1 in the clinic is predicted to more than double the overall response rate (ORR), duration of response (DoR) and progression-free survival (PFS) compared to TYRP1-TCB monotherapy. As a result, it is highly recommended to consider development of CD3-TCBs as part of a combination therapy from the outset, without the need to escalate the CD3-TCB up to the Maximum Tolerated Dose (MTD) in monotherapy and without gating the combination only on RECIST-derived efficacy metrics.

    Place, publisher, year, edition, pages
    Springer Nature, 2022
    Keywords
    CD3-bispecifics, Checkpoint inhibitors, Combination, PKPD modeling
    National Category
    Cancer and Oncology
    Identifiers
    urn:nbn:se:uu:diva-487111 (URN)10.1208/s12248-022-00755-5 (DOI)000865049800002 ()36207642 (PubMedID)
    Note

    Correction in: The AAPS Journal volume 25, Article number: 34 (2023)

    DOI: 10.1208/s12248-023-00802-9

    Available from: 2022-10-25 Created: 2022-10-25 Last updated: 2024-12-10Bibliographically approved
    2. A model‐based approach leveraging in vitro data to support dose selection from the outset: A framework for bispecific antibodies in immuno‐oncology
    Open this publication in new window or tab >>A model‐based approach leveraging in vitro data to support dose selection from the outset: A framework for bispecific antibodies in immuno‐oncology
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    2023 (English)In: CPT: Pharmacometrics and Systems Pharmacology (PSP), E-ISSN 2163-8306, Vol. 12, no 11, p. 1804-1818Article in journal (Refereed) Published
    Abstract [en]

    FAP-4-1BBL is a bispecific antibody exerting 4-1BB-associated T-cell activation only while simultaneously bound to the fibroblast activation protein (FAP) receptor, expressed on the surface of cancer-associated fibroblasts. The trimeric complex formed when FAP-4-1BBL is simultaneously bound to FAP and 4-1BB represents a promising mechanism to achieve tumor-specific 4-1BB stimulation. We integrated in vitro data with mathematical modeling to characterize the pharmacology of FAP-4-1BBL as a function of trimeric complex formation when combined with the T-cell engager cibisatamab. This relationship was used to prospectively predict a range of clinical doses where trimeric complex formation is expected to be at its maximum. Depending on the dosing schedule and FAP-4-1BBL plasma: tumor distribution, doses between 2 and 145 mg could lead to maximum trimeric complex formation in the clinic. Due to the expected variability in both pharmacokinetic and FAP expression in the patient population, we predict that detecting a clear dose-response relationship would remain difficult without a large number of patients per dose level, highlighting that mathematical modeling techniques based on in vitro data could aid dose selection.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2023
    National Category
    Pharmaceutical Sciences Cancer and Oncology
    Research subject
    Pharmaceutical Science
    Identifiers
    urn:nbn:se:uu:diva-526758 (URN)10.1002/psp4.13065 (DOI)001104639100001 ()37964753 (PubMedID)
    Available from: 2024-04-17 Created: 2024-04-17 Last updated: 2024-12-10Bibliographically approved
    3. Combining mathematical modeling, in vitro data and clinical target expression to support bispecific antibody binding affinity selection: a case example with FAP-4-1BBL
    Open this publication in new window or tab >>Combining mathematical modeling, in vitro data and clinical target expression to support bispecific antibody binding affinity selection: a case example with FAP-4-1BBL
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    2024 (English)In: Frontiers in Pharmacology, E-ISSN 1663-9812, Vol. 15, article id 1472662Article in journal (Refereed) Published
    Abstract [en]

    The majority of bispecific costimulatory antibodies in cancer immunotherapy are capable of exerting tumor-specific T-cell activation by simultaneously engaging both tumor-associated targets and costimulatory receptors expressed by T cells. The amount of trimeric complex formed when the bispecific antibody is bound simultaneously to the T cell receptor and the tumor-associated target follows a bell-shaped curve with increasing bispecific antibody exposure/dose. The shape of the curve is determined by the binding affinities of the bispecific antibody to its two targets and target expression. Here, using the case example of FAP-4-1BBL, a fibroblast activation protein alpha (FAP)-directed 4-1BB (CD137) costimulator, the impact of FAP-binding affinity on trimeric complex formation and pharmacology was explored using mathematical modeling and simulation. We quantified (1) the minimum number of target receptors per cell required to achieve pharmacological effect, (2) the expected coverage of the patient population for 19 different solid tumor indications, and (3) the range of pharmacologically active exposures as a function of FAP-binding affinity. A 10-fold increase in FAP-binding affinity (from a dissociation constant [KD] of 0.7 nM–0.07 nM) was predicted to reduce the number of FAP receptors needed to achieve 90% of the maximum pharmacological effect from 13,400 to 4,000. Also, the number of patients with colon cancer that would achieve 90% of the maximum effect would increase from 6% to 39%. In this work, a workflow to select binding affinities for bispecific antibodies that integrates preclinical in vitro data, mathematical modeling and simulation, and knowledge on target expression in the patient population, is provided. The early implementation of this approach can increase the probability of success with cancer immunotherapy in clinical development.

    Place, publisher, year, edition, pages
    Frontiers Media S.A., 2024
    Keywords
    immunotherapy, bispecific antibody, modeling, simulation, binding affinity, oncology, pharmacodynamics, FAP-4-1BBL
    National Category
    Cancer and Oncology
    Identifiers
    urn:nbn:se:uu:diva-542797 (URN)10.3389/fphar.2024.1472662 (DOI)001340381000001 ()39444607 (PubMedID)
    Available from: 2024-11-15 Created: 2024-11-15 Last updated: 2024-12-10Bibliographically approved
    4. A model-based approach to evaluate anti-drug antibody impact on drug exposure with biologics: a case example with the CD3 T-cell bispecific cibisatamab
    Open this publication in new window or tab >>A model-based approach to evaluate anti-drug antibody impact on drug exposure with biologics: a case example with the CD3 T-cell bispecific cibisatamab
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-544013 (URN)
    Available from: 2024-11-27 Created: 2024-11-27 Last updated: 2024-12-10
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  • Public defence: 2025-02-14 09:15 A1:111a, BMC, Uppsala
    Bergman, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology and Immunology.
    Identification and functional characterization of RNA-binding proteins in Salmonella2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacteria live in an ever-changing environment, and thus require adequate gene expression changes to survive and adapt in variable conditions. Regulation of gene expression occurs at several levels. The work presented in this thesis concerns post-transcriptional regulation, i.e. regulation that acts on the transcribed mRNA. The main players at this level of regulation are regulatory small RNAs and RNA-binding proteins (RBPs), which affect mRNA translation and degradation rates. 

    This work has mainly focused on characterizing the globally acting RBP ProQ in Salmonella enterica serovar Typhimurium (S.Tm). ProQ interacts with hundreds of RNA transcripts and is important for many phenotypical traits such as motility, virulence and persister cell formation. In paper I, we identify the interactome of ProQ in infection-like conditions that mimic the Salmonella-containing vacuole (SCV) of eukaryotic host cells. We also highlight ProQ’s relevance for proper expression of the virulence genes connected to survival and proliferation within the SCV, by post-transcriptionally affecting expression of the important regulator PhoP. In paper II, we demonstrate that ProQ promotes biofilm formation in S.Tm, and present a new molecular mechanism of ProQ’s interaction with intrinsic terminators. Upon binding, ProQ hinders poly(A) polymerase I-dependent polyadenylation and thereby protects against 3’end-dependent degradation. In paper III, we implement our RNA interactome capture method in S.Tm, and thereby expand the RNA-binding proteome. Among the identified RBPs we discovered virulence-associated proteins previously not connected to RNA binding activities.

    In conclusion, the work in this thesis shows new aspects concerning the function of ProQ, highlights the physiological relevance of this protein, and generally expands the RNA-binding proteome of S.Tm. Importantly, the findings presented here point to new scientific questions that will help drive future research in the area of post-transcriptional gene regulation.

    List of papers
    1. ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis
    Open this publication in new window or tab >>ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis
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    2024 (English)In: mSphere, E-ISSN 2379-5042, Vol. 9, no 3, article id e00018-24Article in journal (Refereed) Published
    Abstract [en]

    Gastrointestinal disease caused by Salmonella enterica is associated with the pathogen's ability to replicate within epithelial cells and macrophages. Upon host cell entry, the bacteria express a type-three secretion system encoded within Salmonella pathogenicity island 2, through which host-manipulating effector proteins are secreted to establish a stable intracellular niche. Transcription of this intracellular virulence program is activated by the PhoPQ two-component system that senses the low pH and the reduced magnesium concentration of host cell vacuoles. In addition to transcriptional control, Salmonella commonly employ RNA-binding proteins (RBPs) and small regulatory RNAs (sRNAs) to regulate gene expression at the post-transcriptional level. ProQ is a globally acting RBP in Salmonella that promotes expression of the intracellular virulence program, but its RNA repertoire has previously been characterized only under standard laboratory growth conditions. Here, we provide a high-resolution ProQ interactome during conditions mimicking the environment of the Salmonella-containing vacuole (SCV), revealing hundreds of previously unknown ProQ binding sites in sRNAs and mRNA 3 ' UTRs. ProQ positively affected both the levels and the stability of many sRNA ligands, some of which were previously shown to associate with the well-studied and infection-relevant RBP Hfq. We further show that ProQ activates the expression of PhoP at the post-transcriptional level, which, in turn, leads to upregulation of the intracellular virulence program.

    Place, publisher, year, edition, pages
    American Society for Microbiology, 2024
    Keywords
    ProQ, CLIP-seq, RNA-binding protein, small RNA, Salmonella, virulence, PhoP
    National Category
    Microbiology in the medical area Microbiology
    Identifiers
    urn:nbn:se:uu:diva-528156 (URN)10.1128/msphere.00018-24 (DOI)001177434900002 ()38411119 (PubMedID)
    Funder
    Swedish Research Council, 2016-03656Swedish Research Council, 2021-04657Swedish Research Council, 2018-02223Swedish Foundation for Strategic Research, ICA16-0021Åke Wiberg FoundationWenner-Gren Foundations
    Available from: 2024-05-22 Created: 2024-05-22 Last updated: 2024-12-11Bibliographically approved
    2. ProQ prevents mRNA degradation through inhibition of poly(A) polymerase
    Open this publication in new window or tab >>ProQ prevents mRNA degradation through inhibition of poly(A) polymerase
    (English)Manuscript (preprint) (Other academic)
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-544955 (URN)
    Available from: 2024-12-10 Created: 2024-12-10 Last updated: 2024-12-11
    3. RNA interactome capture in Salmonella identifies a conserved family of virulence-associated RNA-binding proteins
    Open this publication in new window or tab >>RNA interactome capture in Salmonella identifies a conserved family of virulence-associated RNA-binding proteins
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:uu:diva-544958 (URN)
    Available from: 2024-12-10 Created: 2024-12-10 Last updated: 2024-12-11
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  • Public defence: 2025-02-14 09:15 10132, Häggsalen, Ångströmlaboratoriet, Uppsala
    Holeňák, Radek
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics.
    Close encounters: electronic excitations by keV ions in single crystals2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the study of ion-solid interactions, particularly at ion energies of several tens of keV. In this regime, ion beams hold technological potential for high-resolution depth profiling as well as for increased precision in ion implantation, which is paramount for applications in semiconductor manufacturing or quantum computing. The understanding of the exact nature of energy dissipation processes active during ion penetration is crucial for technological advancement but simultaneously presents a fundamental physics problem worth investigating. A widely accepted picture describing keV ion-solid interactions is the one of electronic excitations in an electron gas. Nevertheless, the experimentally accessible observables, such as energy or charge transfer, show unexpectedly clear signs of an atomic signature in the individual interaction. The origin of these processes is currently under investigation both in dedicated experiments and using novel computational approaches.

    The research employs ion transmission experiments through thin self-supporting single-crystalline membranes which allow for a confinement of interaction distances and thus processes. Ions experiencing close collisions with target atoms displays energy losses beyond those expected in the electron gas picture. Correlating these observations with the charge state distributions of the transmitted projectiles underscores the role of close collisions facilitating the formation of molecular orbitals. A quantitative analysis reveals this atomistic nature of the interaction being the dominant energy dissipation channel for slow, heavy ions.

    The Time-of-Flight Medium-Energy Ion Scattering system (ToF-MEIS) at Uppsala University was used as a primary tool for the investigations. The present work further developed this instrumentation as well as established new ion-based analytical techniques in-situ. Control over the surface composition is mandatory to yield reliable empirical data in the investigations presented in this thesis. Elastic recoil detection was shown capable of quantitative analysis of light surface contaminants, both on bulk and transmission samples. Ion-induced surface sputtering and desorption were employed on self-supporting membranes shedding light on the underlying mechanism for the desorption process. Finally, the construction and commissioning of an advanced UHV preparation chamber opened up for in-situ synthesis and modification of materials, which in combination with ToF-MEIS enables precise compositional and structural analysis at a nanometre scale. 

    List of papers
    1. Sensitive multi-element profiling with high depth resolution enabled by time-of-flight recoil detection in transmission using pulsed keV ion beams
    Open this publication in new window or tab >>Sensitive multi-element profiling with high depth resolution enabled by time-of-flight recoil detection in transmission using pulsed keV ion beams
    2022 (English)In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 204, article id 111343Article in journal (Refereed) Published
    Abstract [en]

    The potential of time-of-flight recoil detection for sensitive multi-element profiling of thin membranes and quasi -2D systems in transmission geometry using pulsed keV ion beams is assessed. While the time-of-flight approach allows for simultaneous detection of multiple elements, to the largest extent irrespective of recoil charge states, the keV projectile energies guarantee high recoil-cross sections yielding high sensitivity at low dose. We demonstrate the capabilities of the approach using 22Ne and 40Ar as projectiles transmitted through thin carbon foils featuring optional LiF-coatings and single-crystalline silicon membranes for different sample preparation routines and crystal orientations.Using a large position-sensitive detector (0.13 sr), a depth resolution below 6 nm and sensitivity below 1014 atoms/cm2 was achieved for H in a 50 nm thick silicon membrane. For crystalline targets, we show how the probability of creation and detection of recoils and their observed angular distribution depend on sample orientation.

    Place, publisher, year, edition, pages
    Elsevier, 2022
    Keywords
    Recoils, keV ions, Self-supporting films, Time-of-flight
    National Category
    Subatomic Physics
    Identifiers
    urn:nbn:se:uu:diva-497717 (URN)10.1016/j.vacuum.2022.111343 (DOI)000927565000003 ()
    Funder
    Swedish Research Council, 2017-00646_9Swedish Research Council, 2019-00191Swedish Foundation for Strategic Research, RIF14-0053
    Available from: 2023-03-07 Created: 2023-03-07 Last updated: 2024-12-12Bibliographically approved
    2. The influence of geometry and specific electronic and nuclear energy deposition on ion-stimulated desorption from thin self-supporting membranes
    Open this publication in new window or tab >>The influence of geometry and specific electronic and nuclear energy deposition on ion-stimulated desorption from thin self-supporting membranes
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Fusion, Plasma and Space Physics
    Identifiers
    urn:nbn:se:uu:diva-545202 (URN)
    Available from: 2024-12-12 Created: 2024-12-12 Last updated: 2024-12-18Bibliographically approved
    3. Simultaneous assessment of energy, charge state and angular distribution for medium energy ions interacting with ultra-thin self-supporting targets: A time-of-flight approach
    Open this publication in new window or tab >>Simultaneous assessment of energy, charge state and angular distribution for medium energy ions interacting with ultra-thin self-supporting targets: A time-of-flight approach
    2021 (English)In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 185, article id 109988Article in journal (Refereed) Published
    Abstract [en]

    We demonstrate simultaneous measurements of the charge state, energy and angular distribution of keV ions in transmission experiments through self-supporting foils. Using a time-of-flight approach we have introduced an electrostatic deflection apparatus as an extension to existing medium energy ion scattering (MEIS) instrumentation. Different positive, neutral and negative charge states have been discriminated and quantified for initially singly charged beams of He, N, O and Ne in the energy range from 25 to 250 keV. In parallel, the ion energy after interaction with the target has been assessed for all detected particles, while particles can be discriminated by deflection angle. Self-supporting thin carbon foils were used as samples to benchmark our experiments with literature data where available.

    Place, publisher, year, edition, pages
    ElsevierPERGAMON-ELSEVIER SCIENCE LTD, 2021
    Keywords
    Charge fraction, keV ions, Self-supporting films, Carbon, Time-of-flight
    National Category
    Fusion, Plasma and Space Physics
    Identifiers
    urn:nbn:se:uu:diva-437718 (URN)10.1016/j.vacuum.2020.109988 (DOI)000618234900005 ()
    Funder
    Swedish Research Council, 2017-00646_9Swedish Foundation for Strategic Research , RIF14-0053
    Available from: 2021-03-15 Created: 2021-03-15 Last updated: 2024-12-12Bibliographically approved
    4. A new system for sample synthesis, preparation and modification combined with in-situ depth profiling using medium energy ions
    Open this publication in new window or tab >>A new system for sample synthesis, preparation and modification combined with in-situ depth profiling using medium energy ions
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    2025 (English)In: Vacuum, ISSN 0042-207X, E-ISSN 1879-2715, Vol. 231, article id 113824Article in journal (Refereed) Published
    Abstract [en]

    We present equipment for sample synthesis, preparation and modification enabling in-situ studies employing medium energy ion beams at the ion implanter facility of the Tandem Laboratory national research infrastructure at Uppsala University. The integral instrumentation enables controlled thin-film synthesis, modification and characterization applicable to study near-surface processes such as thin-film growth, phase transformation, oxidation, annealing, catalysis or ion implantation. We describe the available instrumentation with its specifications and present four demonstrative experiments with a particular focus on the acquired in-situ capabilities addressing 1) Evaporation and thermal alloying of thin films - nickel silicides 2) Reactive magnetron sputtering and controlled oxidization - photochromic YHO 3) Sputtering and low-energy implantation - hydrogen in tungsten and 4) Surface cleaning of sensitive systems - self-supporting silicon membranes.

    Place, publisher, year, edition, pages
    Elsevier, 2025
    National Category
    Materials Chemistry Condensed Matter Physics Fusion, Plasma and Space Physics
    Identifiers
    urn:nbn:se:uu:diva-544238 (URN)10.1016/j.vacuum.2024.113824 (DOI)001358772200001 ()2-s2.0-85208767832 (Scopus ID)
    Funder
    Swedish Research Council, 2019-00191
    Available from: 2024-12-04 Created: 2024-12-04 Last updated: 2024-12-12Bibliographically approved
    5. Contrast modes in a 3D ion transmission approach at keV energies
    Open this publication in new window or tab >>Contrast modes in a 3D ion transmission approach at keV energies
    2020 (English)In: Ultramicroscopy, ISSN 0304-3991, E-ISSN 1879-2723, Vol. 217, article id 113051Article in journal (Refereed) Published
    Abstract [en]

    We present options for visualizing contrast maps in 3D ion transmission experiments. Simultaneous measurement of angular distributions and flight time of ions transmitted through self-supporting, single-crystalline silicon foils allows for mapping of intensity and different energy loss moments. The transmitted projectiles were detected mainly for random beam-sample orientation using pulsed beams of He ions and protons with incident energies 50 and 200 keV. Differences in contrast, observed when varying the projectile type and energy, can be attributed to sample nuclear and electronic structure and bear witness to impact parameter dependent energy loss processes. Our results provide a base for interpretation of data obtained in prospective transmission studies when for example using a helium ion microscope.

    Keywords
    Ion transmission, Energy loss, Contrast maps, Imaging
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:uu:diva-427109 (URN)10.1016/j.ultramic.2020.113051 (DOI)000588011200003 ()32615322 (PubMedID)
    Funder
    Swedish Research Council, 2016-03432_3Swedish Research Council, 2017-00646_9Swedish Foundation for Strategic Research , RIF14-0053
    Available from: 2020-12-17 Created: 2020-12-17 Last updated: 2024-12-12Bibliographically approved
    6. On the correlation of angular distributions of keV ions and trajectory-dependent electronic excitations in transmission channelling geometry
    Open this publication in new window or tab >>On the correlation of angular distributions of keV ions and trajectory-dependent electronic excitations in transmission channelling geometry
    2022 (English)In: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 2326, no 1, article id 012008Article in journal (Refereed) Published
    Abstract [en]

    We use energy discrimination of keV ions transmitted through a thin, single-crystalline silicon membrane to correlate specific angular distribution patterns formed in channelling geometry with trajectory-dependent electronic energy loss. The integral energy and intensity distribution of transmitted ions can thus be dissected into on one side axially channelled projectiles travelling along rather straight trajectories and on the other side dechannelled projectiles predominantly experiencing blocking. Angular distributions of transmitted ions are further simulated with two different Monte-Carlo codes.

    Place, publisher, year, edition, pages
    Institute of Physics Publishing (IOPP), 2022
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-545190 (URN)10.1088/1742-6596/2326/1/012008 (DOI)2-s2.0-85142614630 (Scopus ID)
    Conference
    25th International Conference on Ion Beam Analysis & 17th International Conference on Particle Induce X-ray Emission & International Conference on Secondary Ion Mass Spectrometry (IBA-PIXE & SIMS 2021), 11-15 October 2021, Online
    Funder
    Swedish Research Council, 2017-00646_9Swedish Research Council, 2019-00191Swedish Foundation for Strategic Research, RIF14-0053
    Available from: 2024-12-12 Created: 2024-12-12 Last updated: 2024-12-13Bibliographically approved
    7. Assessing trajectory-dependent electronic energy loss of keV ions by a binary collision approximation code
    Open this publication in new window or tab >>Assessing trajectory-dependent electronic energy loss of keV ions by a binary collision approximation code
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    2024 (English)In: Physical Review Applied, E-ISSN 2331-7019, Vol. 21, no 2, article id 024048Article in journal (Refereed) Published
    Abstract [en]

    The inelastic energy deposition of energetic ions is a decisive quantity for numerous industrial-scale applications, such as sputtering and ion implantation, yet the underlying physics being governed by dynamic many-particle processes is commonly only qualitatively understood. Recently, transmission experiments on single-crystalline targets (Phys. Rev. Lett. 124, 096601 & Phys. Rev. A 102, 062803) revealed a complex energy scaling of the inelastic energy loss of low-energy ions heavier than protons along different trajectories. We use a Monte Carlo like binary collision approximation code equipped with an impact-parameter-dependent modeling of the inelastic energy losses to assess the role of local contributions to electronic excitations in these cases. We compare angular intensity distributions of calculated trajectories with experimental results for 50-keV 4He and 100-keV 29Si ions transmitted in a time-of-flight setup through single-crystalline silicon (001) foils with nominal thicknesses of 200 and 50 nm, respectively. In these calculations, we employ different models of electronic energy loss, i.e., local and nonlocal forms for light and heavy projectiles. We find that the vast number of projectiles are eventually channeled along their trajectories, regardless of the alignment of the crystal with respect to the incident beam. It is, however, only when local electronic energy loss is considered that the simulated two-dimensional maps and energy distributions show excellent agreement with the experimental results, where channeling leads to significantly reduced stopping, especially for heavier projectiles. We demonstrate the relevance of these effects for ion implantations by assessing the nonlinear and nonmonotonic scaling of the ion range with the thickness of a random surface layer.

    Place, publisher, year, edition, pages
    American Physical Society, 2024
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-526180 (URN)10.1103/PhysRevApplied.21.024048 (DOI)001187487900002 ()
    Funder
    Swedish Research Council, 2019-00191Swedish Foundation for Strategic Research, RIF14-0053
    Available from: 2024-04-08 Created: 2024-04-08 Last updated: 2024-12-12Bibliographically approved
    8. Trajectory dependence of electronic energy-loss straggling at keV ion energies
    Open this publication in new window or tab >>Trajectory dependence of electronic energy-loss straggling at keV ion energies
    2023 (English)In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 107, no 8, article id 085110Article in journal (Refereed) Published
    Abstract [en]

    We have measured the electronic energy-loss straggling of protons, helium, boron, and silicon ions in silicon using a transmission time-of-flight approach. Ions with velocities between 0.25 and 1.6 times the Bohr velocity were transmitted through single-crystalline Si(100) nanomembranes in either channeling or random geometry to study the impact parameter dependence of energy-loss straggling. Nuclear and path length contributions to the straggling were determined with the help of Monte Carlo simulations. Our results exhibit an increase in straggling with increasing ion velocity for channeled trajectories for all projectiles as well as for protons and helium in random geometry. In contrast for heavier ions, electronic straggling at low velocities does not decrease further but plateaus and even seems to increase again. We compare our experimental results with transport cross section calculations. The satisfying agreement for helium shows that electronic stopping for light ions is dominated by electron-hole pair excitations, and that the previously observed trajectory dependence can indeed be attributed to a higher mean charge state for random trajectories. No agreement is found for boron and silicon indicating the breakdown of models based solely on electron-hole pair excitations, and that local electron-promotion and charge-exchange events significantly contribute to energy loss at low velocities.

    Place, publisher, year, edition, pages
    American Physical Society, 2023
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-498558 (URN)10.1103/PhysRevB.107.085110 (DOI)000934255800002 ()
    Funder
    Swedish Research Council, 2017-00646_9Swedish Research Council, 2019_00191Swedish Foundation for Strategic Research, RIF14-0053
    Available from: 2023-03-17 Created: 2023-03-17 Last updated: 2024-12-12Bibliographically approved
    9. Charge state distributions of Xenon ions with keV kinetic energies transmitted through graphene and carbon self-supporting foils
    Open this publication in new window or tab >>Charge state distributions of Xenon ions with keV kinetic energies transmitted through graphene and carbon self-supporting foils
    2024 (English)In: Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, ISSN 0168-583X, E-ISSN 1872-9584, Vol. 554, article id 165415Article in journal (Refereed) Published
    Abstract [en]

    We investigated the charge state distributions and energy loss of single and double-charged Xenon ions (20-220 keV) passing through graphene, Quantifoil, and 10 nm thick carbon membranes. Utilizing simultaneous carbon recoil detection on the graphene-containing sample, we determined the areal density of carbon equivalent to 3 monolayers of graphene, indicating only slight contamination by e.g. PMMA, of our exiting surfaces. The charge state distributions revealed notable proportions of higher charge states, up to Xe+5 at higher energies, with mean charge states consistently below 1. The observed exponential decrease in higher charge fractions suggests electron stripping processes play a significant role. Differences in mean charge states are found among the three systems studied.

    Place, publisher, year, edition, pages
    Elsevier, 2024
    Keywords
    Ion transmission, Equilibrium charge state, Xenon, Charge -exchange, Graphene
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-534758 (URN)10.1016/j.nimb.2024.165415 (DOI)001251497800001 ()
    Funder
    Swedish Research Council, 2019-00191
    Available from: 2024-07-11 Created: 2024-07-11 Last updated: 2024-12-12Bibliographically approved
    10. Charge state dynamics of keV ions in solids
    Open this publication in new window or tab >>Charge state dynamics of keV ions in solids
    (English)Manuscript (preprint) (Other academic)
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-545205 (URN)
    Available from: 2024-12-12 Created: 2024-12-12 Last updated: 2024-12-18Bibliographically approved
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  • Public defence: 2025-02-14 10:15 Humanistiska teatern, Uppsala
    Grönroos, Ida
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of ALM.
    “I Can't Play God, You Know”: Ethical Dilemmas that Archivists Face in the Assessment of Records from Social and Psychiatric Care2025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    When a person requests records from a public archives in Sweden, the records must be assessed, and any information in them that may be detrimental for the person concerned shall be redacted before disclosure. This puts the assessing civil servants—in this study, archivists working at municipal and regional Swedish archives—in a position between the individual asking for information, and the state holding it. When requested records concern social care or health care, the assessments become part of the state’s interventions in the most private of spheres that exist: the family and the body. The assessing archivists often find themselves caught up in conflicts between the archive users’ rights to knowledge about their lives and other people’s right to privacy.

    This dissertation focuses on these archivists as street-level bureaucrats. Their role is to put legislation into practice and make day-to-day decisions, often using a great deal of professional discretion. Starting from the position that (public sector) archives operate in the tension field between the individual and state power, the dissertation explores how different views on vulnerability, social care, privacy, and dignity affect the assessing, classifying, and disclosing of official records containing sensitive personal information. In the interviewed archivists’ reasoning on detriment assessment and disclosure, two ethical perspectives, the legalistic ethics and the feminist ethics of care, are brought to the fore. The aim of the present study is not to reach a conclusion about which ethical perspective is “right,” but to show how the feminist ethics of care clash with the established legalistic ethics.

    The leeway that archivists have for professional discretion gives them power. The inherent paradox of power in the archives in combination with the intricate webs of relationships that are documented in care records, leave archivists stranded. Neither the legalistic ethics nor the feminist ethics of care are sufficient for providing guidance about decisions on disclosure. Whichever way the archivists turn, they are left with undesirable consequences and unsolvable problems. Thus trapped, the archivists in this study must walk a fine line between care and control, between the rule of law and inhumane bureaucracy.

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  • Public defence: 2025-02-14 10:15 Universitetshuset sal IX, Uppsala
    Olenius, Ida
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology, Church History and Mission History.
    Andlig beredskap: Svenska kyrkans arbete för folkets inre försvarskraft under andra världskriget, 1939–19452025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The study investigates how and why representatives of the Church of Sweden attempted to contribute to Sweden’s defence during World War II by raising people’s fortitude and will for defence, thus highlighting the role of the Church in modern Swedish society and nation-building. 

    The wartime period is divided into five parts based on historical events that influenced the Swedish perception of threat from foreign powers. For each subperiod, the initiatives taken by Church actors are investigated and the forms of work, actors, formal structures, and networks are mapped out. Particular interest is paid to Church representatives’ use and interpretation of slogans such as “spiritual preparedness” and “the Christian principle”. 

    The source material consists of minutes, correspondence, memoranda, reports, petitions, manifestos, public speeches and statements, newspaper and magazine articles, books, pamphlets, and films. Several theoretical perspectives are combined, with Pierre Bourdieu’s field theory as the basis. The Church of Sweden is viewed as a social field competing against other fields, most noticeably those of the state and the dissenter movements, for certain capitals in an “arena of spiritual preparedness”. This struggle involves the use and exchange of resources that are either particular to the Church or available through interactions with the other fields. 

    Among the actors within the Church of Sweden who took up the call to strengthen the people’s fortitude were bishops, clergymen, and laypeople, who worked individually, in groups, through a temporary formal organisation, or the Oxford group movement. They used a combination of traditional and innovative work forms that changed over time and highlighted the Church’s practical as well as motivational resources. They wished to demonstrate that the Church of Sweden was an integral part of Swedish national history, culture, and identity. This understanding was contested by outsiders as well as by actors within the Church, who either opposed the conservative, church-oriented vision of the nation that was often expressed or warned against the risk of instrumentalising the Church for the purposes of the state. 

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  • Public defence: 2025-02-14 10:15 Ihresalen, Uppsala
    Andersson, Roland
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Scandinavian Languages.
    Ekberg, Ljung och Rattfält: Soldatnamn i Värmland 1684–19002025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    The aim of this dissertation in the field of onomastics is to examine the presence of soldiers’ names and to describe patterns and changes of such names in Värmland’s Infantry Regiment and in Värmland’s Riflemen Regiment. The geographical area of interest includes the province of Värmland, parts of the province of Närke, and parts of the province of Dalsland. The examined period regarding the infantry regiment is 1684–1900, and regarding the riflemen regiment 1790–1900. Early soldiers’ names can be adulatory but can also in some cases be derogatory. In the 1684 general inspection list there are also a number of soldiers’ names based on place-names – single-part names or two-part names – such as Elg from the homestead Elgåna and Fiällman from the homestead Fiäll. At Värmland’s regiment soldiers were thereafter given names based on place-names from the homesteads that provided each and every soldier with a soldier’s cottage. Some of the names were changed, often shortened (from two-part names to single-part names), over the years but the connection between soldiers’ names and place-names remained. The Royal Värmland’s riflemen regiment was formed in 1788. Riflemen were all given soldiers’ names, but their names are quite different compared to the infantry soldiers’ names above. Many of the names among the riflemen are similar to contemporary family names (surnames). Some examples are Nyström, Strandberg and Wahlberg. This means that it is necessary to investigate both military and civilian documentation in order to decide whether a certain name was initially a soldier’s name or a family name. At the turn of the century in 1900 the tradition of giving soldiers certain names came to an end. Many of these names are however still in use as family names, which indicates that soldiers and riflemen found their »professional» names worth keeping. All soldiers’ names in this dissertation have been gathered from general inspection lists, that is military sources. 

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  • Public defence: 2025-02-14 13:15 A1:107a, Uppsala
    Panagiotou, Styliani
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology. Uppsala University.
    Inter-organelle crosstalk in the pancreatic β cell: Membrane contact sites as regulators of insulin secretion2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Pancreatic β cells play a crucial role in glucose homeostasis by producing and secreting insulin. Impaired insulin release leads to chronic hyperglycemia and contributes to the development of type 2 diabetes (T2D). Insulin is stored in secretory granules, which are transported to the plasma membrane for exocytosis to the circulation in response to elevated blood glucose levels. The mechanisms that couple glucose metabolism to insulin secretion are complex and involve both Ca2+ and phospholipid signaling. Membrane contact sites (MCSs) are specialized regions where organelle membranes are closely apposed, providing a conduit for non-vesicular lipid exchange and Ca2+ transport between the two compartments, but their importance for normal β cell function is not known. Here, we discover a new type of MCS involving the ER and insulin granules, which facilitate lipid exchange between the two organelles. Oxysterol-binding protein (OSBP), a cytosolic lipid transport protein (LTP), was recruited to these MCSs in a Ca2+- and pH-dependent manner and catalyzed the exchange of granular PI(4)P for ER cholesterol. This mechanism was essential for normal insulin secretion. Transmembrane protein 24 (TMEM24) is an ER-anchored LTP that dynamically interacts with the plasma membrane (PM) and provides it with phosphatidylinositol, a precursor of other phosphoinositides. We found that TMEM24 localization was spatially and temporally regulated by Ca2+ and diacylglycerol (DAG), and that, upon dissociation from the PM, it stabilized at ER-mitochondria MCSs. Loss of TMEM24 led to dysregulation of both ER and mitochondria Ca2+, impaired ATP production, and reduced insulin secretion. High-resolution imaging further revealed that TMEM24 also localized close to a subset of newly synthesized insulin granules that were in proximity to mitochondria. These organelle contacts were additionally defined by the presence of voltage-dependent anion channel (VDAC) and Mitofusin-2 on the mitochondria and the vesicular nucleotide transporter (VNUT) on the insulin granules. Reduced VNUT expression abolished the interaction between mitochondria and insulin granules and led to impaired insulin granule biogenesis and exocytosis. Collectively, our findings highlight the significant roles of different MCSs in maintaining normal β cell function.

     

    List of papers
    1. The endoplasmic reticulum-plasma membrane tethering protein TMEM24 is a regulator of cellular Ca2+ homeostasis
    Open this publication in new window or tab >>The endoplasmic reticulum-plasma membrane tethering protein TMEM24 is a regulator of cellular Ca2+ homeostasis
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    2022 (English)In: Journal of Cell Science, ISSN 0021-9533, E-ISSN 1477-9137, Vol. 135, no 5, article id jcs259073Article in journal (Refereed) Published
    Abstract [en]

    Endoplasmic reticulum (ER)-plasma membrane (PM) contacts are sites of lipid exchange and Ca2+ transport, and both lipid transport proteins and Ca2+ channels specifically accumulate at these locations. In pancreatic beta-cells, both lipid and Ca2+ signaling are essential for insulin secretion. The recently characterized lipid transfer protein TMEM24 (also known as C2CD2L) dynamically localizes to ER-PM contact sites and provides phosphatidylinositol, a precursor of phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol 4,5-bisphosphate [PI(4,5)P-2], to the PM. beta-cells lacking TMEM24 exhibit markedly suppressed glucose-induced Ca2+ oscillations and insulin secretion, but the underlying mechanism is not known. We now show that TMEM24 onlyweakly interacts with the PM, and dissociates in response to both diacylglycerol and nanomolar elevations of cytosolic Ca2+. Loss of TMEM24 results in hyper-accumulation of Ca2+ in the ER and in excess Ca2+ entry into mitochondria, with resulting impairment in glucose-stimulated ATP production.

    Place, publisher, year, edition, pages
    The Company of Biologists, 2022
    Keywords
    Membrane contact sites, Ca2+, Insulin secretion, Phosphoinositides, Mitochondria
    National Category
    Cell and Molecular Biology Cell Biology
    Identifiers
    urn:nbn:se:uu:diva-473970 (URN)10.1242/jcs.259073 (DOI)000783839400023 ()34821358 (PubMedID)
    Funder
    Swedish Research Council, 2019-01456Diabetesfonden, DIA2018-332
    Available from: 2022-05-06 Created: 2022-05-06 Last updated: 2024-12-10Bibliographically approved
    2. OSBP-mediated PI(4)P-cholesterol exchange at endoplasmic reticulum-secretory granule contact sites controls insulin secretion
    Open this publication in new window or tab >>OSBP-mediated PI(4)P-cholesterol exchange at endoplasmic reticulum-secretory granule contact sites controls insulin secretion
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    2024 (English)In: Cell Reports, E-ISSN 2211-1247, Vol. 43, no 4, article id 113992Article in journal (Refereed) Published
    Abstract [en]

    Insulin is packaged into secretory granules that depart the Golgi and undergo a maturation process that involves changes in the protein and lipid composition of the granules. Here, we show that insulin secretory granules form physical contacts with the endoplasmic reticulum and that the lipid exchange protein oxysterol-binding protein (OSBP) is recruited to these sites in a Ca 2+ -dependent manner. OSBP binding to insulin granules is positively regulated by phosphatidylinositol-4 (PI4)-kinases and negatively regulated by the PI4 phosphate (PI(4)P) phosphatase Sac2. Loss of Sac2 results in excess accumulation of cholesterol on insulin granules that is normalized when OSBP expression is reduced, and both acute inhibition and small interfering RNA (siRNA)-mediated knockdown of OSBP suppress glucose -stimulated insulin secretion without affecting insulin production or intracellular Ca 2+ signaling. In conclusion, we show that lipid exchange at endoplasmic reticulum (ER) -granule contact sites is involved in the exocytic process and propose that these contacts act as reaction centers with multimodal functions during insulin granule maturation.

    Place, publisher, year, edition, pages
    Cell Press, 2024
    National Category
    Cell and Molecular Biology Endocrinology and Diabetes
    Identifiers
    urn:nbn:se:uu:diva-528224 (URN)10.1016/j.celrep.2024.113992 (DOI)001215101800001 ()38536815 (PubMedID)
    Funder
    Swedish Research Council, MH-2019-01456Swedish Research Council, 2019-01406Swedish Research Council, 2021-02081
    Note

    Tan, Kia Wee and Nguyen, Phuoc My contributed equally

    Olof Idevall-Hagren corresponding author

    Available from: 2024-05-17 Created: 2024-05-17 Last updated: 2024-12-10Bibliographically approved
    3. Organelle crosstalk controls the early stages of insulin granule maturation
    Open this publication in new window or tab >>Organelle crosstalk controls the early stages of insulin granule maturation
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Insulin secretion from pancreatic β-cells is a tightly controlled process where hormone synthesis, granule formation and release are regulated in order to maintain whole body glucose homeostasis. Failure to produce or release insulin results in hyperglycemia that may develop into diabetes. Insulin-containing granules exist in different pools that have different propensity for release, yet what determined the fate of a granule after initial formation is not clear. In this study we aimed to identify key steps in the early life of an insulin granule that directs it towards release. Using two different methods for time-dependent labeling, we found that insulin granules shortly after budding from the trans-Golgi network associate with both the endoplasmic reticulum and mitochondria. These organelle interactions are defined by enrichment of the lipid transport protein TMEM24, the voltage-dependent anion channel (VDAC), Mitofusin-2 and the vesicular nucleotide transporter (VNUT). Reduced VNUT expression prevented the recruitment of VDAC to insulin granules and resulted in impaired insulin granule biogenesis and insulin secretion. These results show the requirement of multi-organelle crosstalk for normal progression through the early stages of the secretory pathway.

    Keywords
    VNUT, VDAC, Mfn2, membrane contact sites, proinsulin, RUSH
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-542943 (URN)
    Available from: 2024-11-15 Created: 2024-11-15 Last updated: 2024-12-10
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  • Public defence: 2025-02-14 13:15 Sal X, Universitetshuset, Uppsala
    Bennich-Björkman, Anna
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Educational Sciences, Department of Education.
    The Higher Education Norm: Rethinking Paths to Independence and Adulthood in a Former Industrial Community2025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This study investigates the perception and navigation of higher education among young adults in a former industrial community in Sweden. Similar to other countries, the Swedish system of higher education has expanded considerably since the 1960s, to include more students and institutions. Alongside this expansion, a process of de-industrialisation has taken place since the 1970s. The thesis focuses on a locality severely affected by the diminishing of manufacturing industries, where higher education was unusual due to the prevalence of working-class occupations. The study asks how higher education is managed in a context where educational levels are comparatively low and where labour market participation did not previously require tertiary qualifications.

    The thesis is designed as a single-case study of Söderhamn, Sweden. The main method used is in-depth interviews with young adults and parents. Through the study of how young adults reason about education in general, and a potential entry into tertiary education in particular, the thesis analyses how higher education is viewed within this social context. Using social class, gender, and dispositions to interpret the interviewees’ reasoning, the thesis arrives at the conclusion that there exists a higher education norm among young adults in Söderhamn today. Far from everyone will or want to attend university, yet, the study points to the fact that young adults are required to negotiate the norm of higher education, even if they prefer a different path.

    A significant conclusion is that this newly established norm of higher education is intertwined with older norms tied to the locality’s industrial past. Young adults and parents share the view that higher education is necessary for a stable position in the labour market today. Thus, tertiary education is perceived as an instrument for becoming employable, thereby upholding values of independence and adulthood that have existed for longer. The thesis concludes that the processes of de-industrialisation and the expansion of higher education both sustain and create new social norms that affect young adults’ perceptions and navigations of a potential entry into higher education.

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  • Public defence: 2025-02-17 09:15 101121 (Sonja Lyttkens), Ångström, Uppsala
    Mages, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems.
    Inequality is Information: On its Quantification and Decomposition2025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Inequality and information are concepts from largely different communities. Information theory originated as a mathematical tool to study communication systems, while inequality theory evolved in economics and sociology. These areas developed measures to provide important quantitative insights for their respective applications. However, both domains also need the ability to decompose their measures to shed light on the structure of inequality within a population, or to understand how different pieces of information are provided and interact. 

    In 2010, researchers in information theory developed a technique to decompose how information is provided redundantly by multiple sources, uniquely by a particular source, and synergistically by the interactions between sources. The proposed framework found favor in the community, but the decomposition measure was strongly criticized. Despite significant research efforts, no suitable replacement could be found. The primary contribution of this work is a solution to this open question: We developed a decomposition measure to non-negatively quantify the partial contributions of an arbitrary number of sources about a target with practical operational interpretation. 

    Surprisingly, the underlying representation we used for our decomposing is equivalent to the representation for quantifying inequality. This identified relationship between measures of information and inequality enabled the direct transfer of results. Consequently, we generalized established inequality measures into a new family and provided a novel decomposition that characterizes inequality by the redundant, unique, and synergetic interactions between attributes of individuals. Finally, we demonstrate that subgroup decompositions from inequality theory highlight a recursive subgroup structure of information measures. 

    The developed techniques can directly provide novel insights for studying applied questions in complex systems, information theory, economics, and sociology. Our tools enable professionals to gain deeper insights, understand the impact of changes and make informed decisions.

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  • Public defence: 2025-02-18 13:00 Humanistiska teatern, Uppsala
    Lingström, Maria
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology, Ancient History and Conservation. Uppsala universitet.
    Mästerby, 1361: Battlefield Archaeological Perspectives on the Danish Invasion of Gotland2025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    In July 1361, King Valdemar IV of Denmark invaded the island of Gotland, situated in the central Baltic Sea. The overall objective of this thesis is to assess this invasion from a battlefield archaeological perspective, and to re-evaluate theories presented so far, thereby conceivably presenting a more detailed and nuanced image of the events at hand. What stories might the battlefield archaeological material convey? 

    A central aim is to capture the battle events, which took place in Mästerby parish in central Gotland, on the days prior to the Battle at Visby on 27 July. The Mästerby material represents ‘frozen moments,’ which unfolded within hours, minutes, and even merely seconds. It comprises to date circa 500 conflict-related artefacts, which have been located in and near the former wetland of Fjäle myr. The vast majority of the finds are ferrous. They encompass offensive and defensive weaponry, including fragments of swords, spears, crossbows, bolts, mail, and coats of plates. Within the main battle area, small iron and lead projectiles have also been located, which might imply the use of firearms during the invasion. 

    The weaponry artefacts may enable studies of strategical, tactical, technological, and social aspects of the invasion. In order to reach the overall objective of this thesis, I endeavour to answer the following main research questions: How can the battlefield archaeological material from Mästerby contribute to and nuance our knowledge regarding the 1361 invasion? How do the Mästerby battlefield archaeological artefacts relate to the Korsbetningen material, and finally: How can the 1361 invasion and other medieval martial events contribute to our understanding of the Gotlandic society and its martial organisation?

    The finds constitute a ‘time map’ on which battlefield events are traced. They represent direct martial activity, although no 1361-related human remains have been discovered in Mästerby to date. The battlefield in Visby, despite its renown, has not been located on an archaeological basis, whereas the Korsbetningen mass graves comprise a ‘secondary’ martial context, in that both corpses and battle-related objects have been moved from the actual battle site. In the graves, evidence of weapons is indirectly revealed by skeletal-related traumas, i.e. stab and crush marks. Suits of armour, however, were recovered largely intact, as opposed to the Mästerby armour, which is highly fragmented due to its location in arable land. Thus, the Mästerby and the Visby materials comprise ‘two sides of the same coin’. 

    Although impressive, this archaeological and osteological evidence has functioned largely as background material for almost a century, explaining why the Gotlanders lost rather than scrutinising the nature of the said remains. This overshadowing narrative, depicting the islanders as unprepared and badly-equipped, has led research on the Danish Invasion to focus on the Gotlandic defeat as a scientific point of departure. The battlefield archaeological perspective from Mästerby, however, tells a potentially different story, which I endeavour to convey. This thesis might plausibly reveal a more nuanced viewpoint regarding the invasion, the battles fought and the contingents involved. 

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  • Public defence: 2025-02-21 08:00 Häggsalen, Uppsala
    Hägg, Linus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Applied Nuclear Physics.
    Analysis of neutron cameras and spectrometers with digital data acquisition at tokamaks2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The neutron emission from a fusion plasma can be measured with neutron diagnostics and analysed to estimate plasma quantities. This thesis covers the subject of neutron detection methods using scintillators. It follows the detection process from the scintillation phenomenon and the hardware solutions in the data acquisition, to the software data handling and pulse analysis in the data reduction. It also covers the relationship between the measured scintillation light pulse to the incident neutron energy, using light yield calibration methods and system response functions. In particular, this thesis has focused on the development of methods and codes that allows us to exploit the possibilities offered by fully digital data acquisition systems.

    In the latter half of the thesis, these methods are put into practice for two neutron diagnostic systems at JET, the neutron camera and the MPRu neutron spectrometer. The neutron camera is used to estimate the estimate the volume integrated neutron yield. The method was developed in two iterations, and was applied to measurement data from recent JET DD and DT experiment campaigns. In its latest iteration, the method absolutely calibrates the neutron camera. Comparisons with neutron yield estimates from the JET fission chambers reveal inconsistencies between the two instruments, and between the two iterations of the method for the neutron camera. These discoveries prompt further investigation into the method.

    For the MPRu, a framework was developed for estimating two fusion plasma quantities; the plasma rotation and the thermonuclear emission. The line of sight for the MPRu is advantageous for evaluating these quantities in the core of the plasma. The framework shows great promise, and has the potential of providing complementary measurements to diagnostics which have trouble penetrating into the core.

    The techniques developed in this work can be refined for their current use, and may also be adapted for other similar neutron diagnostic systems.

    List of papers
    1. Estimating the neutron yield in a deuterium plasma with the JET neutron camera
    Open this publication in new window or tab >>Estimating the neutron yield in a deuterium plasma with the JET neutron camera
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    2023 (English)In: Review of Scientific Instruments, ISSN 0034-6748, E-ISSN 1089-7623, Vol. 94, no 7, article id 073502Article in journal (Refereed) Published
    Abstract [en]

    The JET neutron camera is a well-established detector system at JET, which has 19 sightlines each equipped with a liquid scintillator. The system measures a 2D profile of the neutron emission from the plasma. A first principle physics method is used to estimate the DD neutron yield that is based on JET neutron camera measurements and is independent of other neutron measurements. This paper details the data reduction techniques, models of the neutron camera, simulations of neutron transport, and detector responses used to this end. The estimate uses a simple parameterized model of the neutron emission profile. The method makes use of the JET neutron camera’s upgraded data acquisition system. It also accounts for neutron scattering near the detectors and transmission through the collimator. These components together contribute to 9% of the detected neutron rate above a 0.5 MeVee energy threshold. Despite the simplicity of the neutron emission profile model, the DD neutron yield estimate falls on average within 10% agreement with a corresponding estimate from the JET fission chambers. The method can be improved by considering more advanced neutron emission profiles. It can also be expanded to estimate the DT neutron yield with the same methodology.

    Place, publisher, year, edition, pages
    American Institute of Physics (AIP), 2023
    National Category
    Fusion, Plasma and Space Physics
    Research subject
    Physics with specialization in Nuclear Physics
    Identifiers
    urn:nbn:se:uu:diva-512384 (URN)10.1063/5.0144654 (DOI)001023449000005 ()
    Available from: 2023-09-25 Created: 2023-09-25 Last updated: 2024-12-19Bibliographically approved
    2. Estimating the neutron yield in a deuterium-tritium plasma with the JET neutron camera
    Open this publication in new window or tab >>Estimating the neutron yield in a deuterium-tritium plasma with the JET neutron camera
    (English)Manuscript (preprint) (Other academic)
    National Category
    Fusion, Plasma and Space Physics
    Identifiers
    urn:nbn:se:uu:diva-545702 (URN)
    Available from: 2024-12-19 Created: 2024-12-19 Last updated: 2024-12-19
    3. Plasma rotation and thermonuclear neutron emission estimates in JET Deuterium Tritium plasmas from neutron spectroscopy
    Open this publication in new window or tab >>Plasma rotation and thermonuclear neutron emission estimates in JET Deuterium Tritium plasmas from neutron spectroscopy
    (English)Manuscript (preprint) (Other academic)
    National Category
    Fusion, Plasma and Space Physics
    Identifiers
    urn:nbn:se:uu:diva-545703 (URN)
    Available from: 2024-12-19 Created: 2024-12-19 Last updated: 2024-12-19
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  • Public defence: 2025-02-21 10:00 Ekmansalen, Uppsala
    Jensen, Axel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Genomics of an African primate radiation2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Rather than presenting as a swarm of continuous trait variation, organisms tend to cluster in discrete groups with similar characteristics. Understanding the emergence and maintenance of these discontinuities, commonly recognized as species, is a fundamental goal in evolutionary biology. In this thesis, I use comparative phylogenomics to elucidate the evolutionary processes shaping the remarkable diversification of guenons (tribe Cercopithecini), a diverse African primate group comprising ~35 species that radiated over the past ~10-12 million years. In Paper I, I present a highly resolved guenon phylogeny, and demonstrate extensive ancestral gene flow, also between deeply divergent lineages with different karyotypes. I found that genomic regions with strong signals of introgression were enriched for immune genes, possibly representing adaptive introgression, and explore potential barriers to gene flow. Paper II focuses on the demography and evolution of the recently described guenon species Cercopithecus lomamiensis, and its sister species C. hamlyni. While both species are listed as vulnerable on the IUCN Red List, I found them to have high genetic diversity, without signs of inbreeding. I also investigate genomic signatures of selection in these species, focusing specifically on putative adaptations to terrestriality, a trait that makes them stand out in the predominantly arboreal genus Cercopithecus. In Paper III, I investigate the prevalence of Y chromosome introgression in guenons, which, in line with the expectations under Haldane’s rule, were rare in this primate group. A notable exception was found in Cercopithecus denti, which carries a Y chromosome that introgressed from C. mitis ~6 million years after their initial divergence. Negligible introgression in autosomal loci suggests that the introgressing Y chromosome reached fixation from a low initial frequency, pointing to a putative selective advantage over the ancestral Y chromosome. Lastly, in Paper IV, I investigate the extensive karyotype diversification among guenons, and whether it played a role in speciation. By assembling the genomes of eight species with different karyotypes, I identified 30 independent chromosomal fission events, and four fusions. I found that introgression was reduced on fissioned relative to conserved chromosomes in a previously identified gene flow event between C. cephus (2n = 66) and C. pogonias (2n = 72), suggesting a potential role of fissions as reproductive barriers. This thesis provides insights into the evolutionary forces that shaped one of the world’s most speciose primate radiations, contributing to a broader understanding of the genetics of species diversification.

     

    List of papers
    1. Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
    Open this publication in new window or tab >>Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
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    2023 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 12, article id msad247Article in journal (Refereed) Published
    Abstract [en]

    Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

    Place, publisher, year, edition, pages
    Oxford University Press, 2023
    Keywords
    phylogenomics, speciation, ancient hybridization, evolutionary genomics, mammalian radiation, guenon
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-518250 (URN)10.1093/molbev/msad247 (DOI)001112259600001 ()37987553 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), SNIC 2022/6-325Swedish National Infrastructure for Computing (SNIC), SNIC 2022/5-561Swedish Research Council, 2018-05973Swedish Research Council, 2020-03398
    Available from: 2023-12-18 Created: 2023-12-18 Last updated: 2024-12-18Bibliographically approved
    2. Sequencing the Cercopithecus lomamiensis holotype provides insights into demography and evolution of a threatened primate lineage
    Open this publication in new window or tab >>Sequencing the Cercopithecus lomamiensis holotype provides insights into demography and evolution of a threatened primate lineage
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-545525 (URN)
    Available from: 2024-12-17 Created: 2024-12-17 Last updated: 2024-12-19
    3. Y chromosome introgression between deeply divergent primate species
    Open this publication in new window or tab >>Y chromosome introgression between deeply divergent primate species
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    2024 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 15, no 1, article id 10398Article in journal (Refereed) Published
    Abstract [en]

    Hybridization and introgression are widespread in nature, with important implications for adaptation and speciation. Since heterogametic hybrids often have lower fitness than homogametic individuals, a phenomenon known as Haldane’s rule, loci inherited strictly through the heterogametic sex rarely introgress. We focus on the Y-chromosomal history of guenons, African primates that hybridized extensively in the past. Although our inferences suggest that Haldane’s rule generally applies, we uncover a Y chromosome introgression event between two species ca. six million years after their initial divergence. Using simulations, we show that selection likely drove the introgressing Y chromosome to fixation from a low initial frequency. We identify non-synonymous substitutions on the novel Y chromosome as candidate targets of selection, and explore meiotic drive as an alternative mechanism. Our results provide a rare example of Y chromosome introgression, showing that the ability to produce fertile heterogametic hybrids likely persisted for six million years in guenons.

    Place, publisher, year, edition, pages
    Springer Nature, 2024
    National Category
    Evolutionary Biology Genetics and Genomics
    Identifiers
    urn:nbn:se:uu:diva-545527 (URN)10.1038/s41467-024-54719-8 (DOI)001367893700007 ()39613758 (PubMedID)2-s2.0-85211111135 (Scopus ID)
    Funder
    Swedish Research Council, 2020-03398Swedish Research Council, 2018-05973Uppsala UniversityKnut and Alice Wallenberg FoundationSwedish National Infrastructure for Computing (SNIC), SNIC 2022/6-325Swedish National Infrastructure for Computing (SNIC), SNIC 2022/5-561UPPMAXStiftelsen Zoologisk Forskning
    Note

    De två sista författarna delar sistaförfattarskapet

    Available from: 2024-12-17 Created: 2024-12-17 Last updated: 2025-01-23Bibliographically approved
    4. Genome evolution in guenons and the role of chromosomal fissions as barriers to gene flow
    Open this publication in new window or tab >>Genome evolution in guenons and the role of chromosomal fissions as barriers to gene flow
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-545526 (URN)
    Available from: 2024-12-17 Created: 2024-12-17 Last updated: 2024-12-18
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  • Public defence: 2025-02-21 10:00 Humanistiska teatern, Uppsala
    Nenzén, Niklas
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Theology, Department of Theology, Systematic Theology.
    Det surrealistiska läsmysteriet: Esoterism, myter och dialektik2025Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Scholars have identified significant intersections between surrealism and Western esotericism. It is often assumed that surrealism prioritizes artistic objectives over occult concerns, due to its clear atheism and scientific, left-leaning perspective, which are thought to conflict with religious beliefs. This study explores these intersections through contemporary theories of Western esotericism studies. From a systematic-theological perspective, surrealist experiences are examined in relation to, rather than in opposition to, esotericism and occultism. A surrealist discourse of ineffable experience is identified – one that aligns with both Western mysticism and the type of esotericism (occultism) that seeks to reenchant the world.

    It is argued that both surrealists and esotericists use magical and imaginative techniques to express the ineffable, addressing the limitations of our conceptual frameworks for understanding experience. To enrich the analysis of these intersections, an esoteric interpretation of Hegel’s thought is offered – particularly his phenomenology – that elucidates and synthesizes his significance for the intellectual traditions and worldviews central to my research project. By analyzing Hegel’s circular and symbolic method, a connection between surrealist Hegelianism, esotericism, and mythology is established, whereby surrealist reading and writing can be seen as an initiatory process that transforms both the individual and society. It is argued that surrealist experience can be understood as a collectively constructed myth that addresses both occult epistemology and sociopolitical concerns.

    The study consists of two case studies: the first one analyzes André Breton’s concept of “the sublime point” and illustrates surrealism’s ongoing discussion of how to handle the demand for absolute and ineffable knowledge. The second one examines surrealism’s collective myth, ”the great transparents”, showing that surrealist mythmaking is tied to an alchemical-hermetic dialectic, also found in Rosicrucianism and post-theosophy, as well as in horror and science fiction literature. The creation of myths here concerns writing the supernatural, which, in turn, writes us — a commitment this study likens to a hermetic reading mystery. The present dissertation thereby contributes to post-Christian theology by discussing art, literature, and poetry from the perspective of surrealism’s atheistic engagement with Christian traditions, particularly the heretical and subversive ones, such as mysticism, hermeticism, alchemy, and post-theosophy.

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  • Public defence: 2025-02-21 13:15 Polhemsalen (10134), Ångströmlaboratoriet, Uppsala
    Olander, Terese
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Observational Astrophysics.
    Characterisation of cool stellar atmospheres for PLATO2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    M dwarfs are the most abundant stars in our Galaxy, but they are not well studied. This is changing as observational capabilities improve and M dwarfs have become important targets in the search for exoplanets. These cool and small stars are therefore key targets in many current and upcoming missions. One such mission is the future ESA telescope PLATO, which aims to find exoplanets using light curves. Thousands of M dwarfs are part of the mission's sample, and all these stars need to be accurately characterised.

    Obtaining accurate atmospheric parameters for M dwarfs using spectroscopy is no easy task. This is because their spectrum is filled with molecular lines due to the low effective temperatures. It is especially challenging in the optical wavelength region, where molecular lines obscure the atomic lines. The situation improves in the near-infrared, which also allows for the benefit of receiving more light.

    In the last decade, many papers deriving M dwarf parameters have been published. These parameters mostly agree within uncertainties, but some discrepancies remain. The first paper presented in this thesis explores these differences while also investigating non-LTE effects in M dwarfs. It finds an insignificant effect for iron but a significant effect for potassium.

    To characterise the thousands of M dwarfs in the PLATO sample, new methods using machine learning have been developed. In the second paper of this thesis, we present a pipeline capable of analysing APOGEE spectra. The pipeline is a modification of an existing FGK version. We trained a new neural network, added a pseudo-continuum correction method, and implemented evolutionary models created for the PLATO mission to obtain the surface gravity. The modified pipeline was tested on a sample of M dwarfs with good results.

    In the final paper presented in this thesis, we provide abundances of Fe, Ti, and Ca for a small sample of well-known M dwarfs using differential abundance analysis. Our results mostly agree within uncertainties when compared to literature values. However, there are few studies to compare with, and there is generally a spread between the available studies.

    List of papers
    1. Comparative high-resolution spectroscopy of M dwarfs: Exploring non-LTE effects
    Open this publication in new window or tab >>Comparative high-resolution spectroscopy of M dwarfs: Exploring non-LTE effects
    2021 (English)In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 649, article id A103Article in journal (Refereed) Published
    Abstract [en]

    Context. M dwarfs are key targets for high-resolution spectroscopy and model atmosphere analyses because of the high incidence of these stars in the solar neighbourhood and their importance as exoplanetary hosts. Several methodological challenges make such analyses difficult, leading to significant discrepancies in the published results.

    Aims. The aim of our work is to compare M dwarf parameters derived by recent high-resolution near-infrared studies with each other and with fundamental stellar parameters. We also assess to what extent deviations from local thermodynamic equilibrium (LTE) for iron and potassium influence the outcome of these studies.

    Methods. We carry out line formation calculations based on a modern model atmosphere grid appropriate for M dwarfs along with a synthetic spectrum synthesis code that treats formation of atomic and molecular lines in cool-star atmospheres including departures from LTE. We use near-infrared spectra collected with the CRIRES instrument at the ESO VLT as reference observational data.

    Results. We find that the effective temperatures obtained with spectroscopic techniques in different studies mostly agree to better than 100 K and are mostly consistent with the fundamental temperatures derived from interferometric radii and bolometric fluxes. At the same time, much worse agreement in the surface gravities and metallicities is evident. Significant discrepancies in the latter parameters appear when results of the studies based on the optical and near-infrared observations are intercompared. We demonstrate that non-LTE effects are negligible for Fe I in M-dwarf atmospheres but are important for K I, which has a number of strong lines in the near-infrared spectra of these stars. These effects, leading to potassium abundance and metallicity corrections on the order of 0.2 dex, may be responsible for some of the discrepancies in the published analyses. Differences in the temperature–pressure structures of the atmospheric models may be another factor contributing to the deviations between the spectroscopic studies, in particular at low metallicities and high effective temperatures.

    Conclusions. High-resolution spectroscopic studies of M dwarfs are yet to reach the level of consistency and reproducibility typical of similar investigations of FGK stars. Attention should be given to details of the line formation physics as well as input atomic and molecular data. Collecting high-quality spectra with a wide wavelength coverage of M dwarfs with known fundamental parameters is an essential step in benchmarking spectroscopic parameter determination of low-mass stars.

    Place, publisher, year, edition, pages
    EDP Sciences, 2021
    Keywords
    techniques: spectroscopic, stars: fundamental parameters, stars: atmospheres, stars: late-type, stars: low-mass
    National Category
    Astronomy, Astrophysics and Cosmology
    Identifiers
    urn:nbn:se:uu:diva-446890 (URN)10.1051/0004-6361/202039747 (DOI)000657613400003 ()
    Funder
    Swedish National Space BoardSwedish Research Council
    Available from: 2021-06-29 Created: 2021-06-29 Last updated: 2024-12-17Bibliographically approved
    2. Performance of the Stellar Abundances and atmospheric Parameters Pipeline adapted for M dwarfs: I. Atmospheric parameters from the spectroscopic module
    Open this publication in new window or tab >>Performance of the Stellar Abundances and atmospheric Parameters Pipeline adapted for M dwarfs: I. Atmospheric parameters from the spectroscopic module
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Astronomy, Astrophysics and Cosmology
    Identifiers
    urn:nbn:se:uu:diva-545381 (URN)
    Available from: 2024-12-16 Created: 2024-12-16 Last updated: 2024-12-17
    3. Abundance analysis of benchmark M dwarfs
    Open this publication in new window or tab >>Abundance analysis of benchmark M dwarfs
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Astronomy, Astrophysics and Cosmology
    Identifiers
    urn:nbn:se:uu:diva-545409 (URN)
    Available from: 2024-12-16 Created: 2024-12-16 Last updated: 2024-12-17
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  • Public defence: 2025-02-21 13:15 Siegbahnsalen 10101, Uppsala
    Eliasson, Nora
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Quantum Dot-Molecular Hybrid Systems for Solar Energy Conversion: Mechanistic Studies to Guide Rational Design2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum dots (QDs) are strong light absorbers with tunable electronic properties. Decoration of QD surfaces with molecular structures offers a versatile approach to directing the behaviour of photogenerated carriers. The studies presented herein are based on semiconductor-molecule hybrid systems tailored for solar energy conversion, where light-harvesting colloidal QDs are combined with molecular compounds on the QD surface. This thesis summary primarily focuses on the dynamics of charge carriers during the initial timescales following photoexcitation, as investigated using femtosecond transient absorption spectroscopy (fs-TA).

    Fs-TA studies of CuInS2 QDs allowed for the identification of a localized hole contribution to the state-filling dynamics in Cu-deficient QDs. Two well-known hydrogen evolving metal complexes based on abundant FeFe and Co were shown to bind strongly to these QDs when mixed in solution. This enabled ultrafast electron transfer (sub-ps to a few ps), monitored directly from reduced catalyst signatures in the visible and mid-infrared region.  The strong binding of the complexes, following a Poisson distribution over the QDs, provided a rationale for their high H2 turnover numbers (~8000 per catalyst). The results reassess the necessity of advanced linking chemistry to overcome diffusion-limited electron transfer to molecular catalysts.

    Further studies demonstrated the potential of rational QD capping ligand design in addressing product selectivity challenges in aqueous photocatalytic CO2 reduction. ZnSe QDs were functionalized with imidazolium-based ligands that promoted CO2 reduction while suppressing H2 evolution. Fs-TA studies and DFT calculations revealed that the strongly bound ligands passivate surface Zn sites, while further stabilizing surface adsorbed CO2-reduction intermediates. 

    Photoelectrical and fs-TA studies of PbS QD solar cells fabricated from different QD sizes revealed that the device performance was limited by band-tail states at the interface between the QD layer and the electron transport material. Interfacial trap states had a greater adverse impact on devices made from larger QDs due to an unfavourable energetic alignment between the layers. Smaller-sized QDs with stronger inter-QD electronic coupling performed better, despite greater energetic disorder within the primary absorption layer. Overall, this thesis work underscores the potential of QD-molecular hybrid systems in solar energy conversion and highlights the potential of ultrafast spectroscopic studies to elucidate the underlying mechanisms and limitations.

    List of papers
    1. Ultrafast Dynamics in Cu-Deficient CuInS2 Quantum Dots: Sub-Bandgap Transitions and Self-Assembled Molecular Catalysts
    Open this publication in new window or tab >>Ultrafast Dynamics in Cu-Deficient CuInS2 Quantum Dots: Sub-Bandgap Transitions and Self-Assembled Molecular Catalysts
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    2021 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 125, no 27, p. 14751-14764Article in journal (Refereed) Published
    Abstract [en]

    The photophysical properties of Cu-deficient Cu01.2In1Sx quantum dots synthesized through a facile aqueous-based procedure have been investigated. Transient absorption experiments were carried out probing in the UV-vis, near-IR, and mid-IR regions, with the aim to (i) study the photophysical properties of the quantum dots and (ii) monitor kinetics of electron transfer to a molecular catalyst. When pumping subbandgap transitions, negative (bleach) signals were observed that were spectrally and kinetically distinct from those observed with bandgap pump wavelengths. Herein, these distinct contributions are suggested to result from the overlapping bleaching of state filling electrons and trapped holes. Such an interpretation highlights the importance of considering the hole-contributions to the bleach for the proper determination of carrier kinetics in similar systems. A model complex of the [Fe-2]-hydrogenase active site was introduced to explore the potential of the quantum dots as photosensitizers for molecular catalysts. The quantum dot photoluminescence was quenched upon catalyst addition, and direct evidence of the singly reduced catalyst was found by transient absorption in the UV-vis and mid-IR. The catalyst accepted reducing equivalents on a subpicosecond time scale upon photoexcitation of the quantum dots, despite no covalent linking chemistry being applied. This implies that charge transfer is not limited by diffusion rates, thus confirming the presence of spontaneous quantum dot and catalyst self-assembly.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS)AMER CHEMICAL SOC, 2021
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-452940 (URN)10.1021/acs.jpcc.1c02468 (DOI)000674871100028 ()
    Funder
    Swedish Energy Agency, 48572-1Knut and Alice Wallenberg FoundationStiftelsen Olle Engkvist Byggmästare
    Available from: 2021-09-13 Created: 2021-09-13 Last updated: 2024-12-20Bibliographically approved
    2. Ultrafast Electron Transfer from CuInS2 Quantum Dots to a Molecular Catalyst for Hydrogen Production: Challenging Diffusion Limitations
    Open this publication in new window or tab >>Ultrafast Electron Transfer from CuInS2 Quantum Dots to a Molecular Catalyst for Hydrogen Production: Challenging Diffusion Limitations
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    2024 (English)In: ACS Catalysis, E-ISSN 2155-5435, Vol. 14, no 6, p. 4186-4201Article in journal (Refereed) Published
    Abstract [en]

    Systems integrating quantum dots with molecular catalysts are attracting ever more attention, primarily owing to their tunability and notable photocatalytic activity in the context of the hydrogen evolution reaction (HER) and CO2 reduction reaction (CO2RR). CuInS2 (CIS) quantum dots (QDs) are effective photoreductants, having relatively high-energy conduction bands, but their electronic structure and defect states often lead to poor performance, prompting many researchers to employ them with a core–shell structure. Molecular cobalt HER catalysts, on the other hand, often suffer from poor stability. Here, we have combined CIS QDs, surface-passivated with l-cysteine and iodide from a water-based synthesis, with two tetraazamacrocyclic cobalt complexes to realize systems which demonstrate high turnover numbers for the HER (up to >8000 per catalyst), using ascorbate as the sacrificial electron donor at pH = 4.5. Photoluminescence intensity and lifetime quenching data indicated a large degree of binding of the catalysts to the QDs, even with only ca. 1 μM each of QDs and catalysts, linked to an entirely static quenching mechanism. The data was fitted with a Poissonian distribution of catalyst molecules over the QDs, from which the concentration of QDs could be evaluated. No important difference in either quenching or photocatalysis was observed between catalysts with and without the carboxylate as a potential anchoring group. Femtosecond transient absorption spectroscopy confirmed ultrafast interfacial electron transfer from the QDs and the formation of the singly reduced catalyst (CoII state) for both complexes, with an average electron transfer rate constant of <kET> ≈ (10 ps)−1. These favorable results confirm that the core tetraazamacrocyclic cobalt complex is remarkably stable under photocatalytic conditions and that CIS QDs without inorganic shell structures for passivation can act as effective photosensitizers, while their smaller size makes them suitable for application in the sensitization of, inter alia, mesoporous electrodes.

    Keywords
    hydrogen, photocatalysis, copper indium sulfide, quantum dots, molecular catalyst, transient absorption, artificial photosynthesis
    National Category
    Physical Chemistry
    Research subject
    Chemistry with specialization in Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-487148 (URN)10.1021/acscatal.3c06216 (DOI)001179811600001 ()38510668 (PubMedID)
    Funder
    EU, Horizon 2020, 765376Swedish Energy Agency, 48572-1
    Note

    Title in dissertation list of articles: Ultrafast Electron Transfer from CuInS2 Quantum Dots to a Molecular Catalyst for Hydrogen Production: Rethinking the Binding Models

    De två första författarna delar förstaförfattarskapet.

    Available from: 2022-10-25 Created: 2022-10-25 Last updated: 2024-12-20Bibliographically approved
    3. Imidazolium-modification enhances photocatalytic CO2 reduction on ZnSe quantum dots
    Open this publication in new window or tab >>Imidazolium-modification enhances photocatalytic CO2 reduction on ZnSe quantum dots
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    2021 (English)In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 12, no 26, p. 9078-9087Article in journal (Refereed) Published
    Abstract [en]

    Colloidal photocatalysts can utilize solar light for the conversion of CO2 to carbon-based fuels, but controlling the product selectivity for CO2 reduction remains challenging, in particular in aqueous solution. Here, we present an organic surface modification strategy to tune the product selectivity of colloidal ZnSe quantum dots (QDs) towards photocatalytic CO2 reduction even in the absence of transition metal co-catalysts. Besides H-2, imidazolium-modified ZnSe QDs evolve up to 2.4 mmol(CO) g(ZnSe)(-1) (TONQD > 370) after 10 h of visible light irradiation (AM 1.5G, lambda > 400 nm) in aqueous ascorbate solution with a CO-selectivity of up to 20%. This represents a four-fold increase in CO-formation yield and 13-fold increase in CO-selectivity compared to non-functionalized ZnSe QDs. The binding of the thiolated imidazolium ligand to the QD surface is characterized quantitatively using H-1-NMR spectroscopy and isothermal titration calorimetry, revealing that a subset of 12 to 17 ligands interacts strongly with the QDs. Transient absorption spectroscopy reveals an influence of the ligand on the intrinsic charge carrier dynamics through passivating Zn surface sites. Density functional theory calculations indicate that the imidazolium capping ligand plays a key role in stabilizing the surface-bound *CO2- intermediate, increasing the yield and selectivity toward CO production. Overall, this work unveils a powerful tool of using organic capping ligands to modify the chemical environment on colloids, thus enabling control over the product selectivity within photocatalyzed CO2 reduction.

    Place, publisher, year, edition, pages
    Royal Society of ChemistryROYAL SOC CHEMISTRY, 2021
    National Category
    Physical Chemistry Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-454302 (URN)10.1039/d1sc01310f (DOI)000658827100001 ()34276937 (PubMedID)
    Funder
    Swedish Energy Agency, 48572-1EU, European Research Council, 68283
    Available from: 2021-09-28 Created: 2021-09-28 Last updated: 2024-12-20Bibliographically approved
    4. Comparing Charge Generation, Transport and Recombination in PbS Quantum Dot Solar Cells Prepared from Two Sizes of Quantum Dots
    Open this publication in new window or tab >>Comparing Charge Generation, Transport and Recombination in PbS Quantum Dot Solar Cells Prepared from Two Sizes of Quantum Dots
    (English)Manuscript (preprint) (Other academic)
    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-545698 (URN)
    Available from: 2024-12-19 Created: 2024-12-19 Last updated: 2024-12-20
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  • Public defence: 2025-02-24 08:30 Universitetshuset (Sal IV), Uppsala
    Hörberg, Niklas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Child and Adolescent Psychiatry.
    Beyond Symptoms – Measuring functioning in psychiatric patients and exploring influencing factors2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Functioning, the ability to perform important tasks in life, varies greatly among psychiatric patients. Factors such as comorbidity, personality disorders, trauma, personality and attachment style have been linked to functioning, but never studied together. This thesis aims to explore functioning in psychiatric patients by validating clinical measurement tools and identifying key factors influencing it.

    Paper I evaluated the psychometric properties of the Sheehan Disability Scale (SDS) in a sample of 160 young psychiatric patients diagnosed with ADHD, Bipolar Disorder, or Borderline Personality Disorder. Exploratory factor analysis confirmed a one-factor structure, and the SDS demonstrated high internal consistency and concurrent validity. The study supports the tool's reliability and utility in clinical settings for assessing functioning.

    Paper II evaluated the psychometric properties of the Early Trauma Inventory (ETI) in 243 young psychiatric patients and 56 controls. The factor analysis confirmed the previously seen four-factor model, and showed good to acceptable fit. Cronbach’s alpha varied between 0.55 and 0.76, with higher values in clinical samples compared to controls. The test-retest reliability was good, and the test could discriminate between groups with different levels of traumatisation, supporting its discriminant validity. The Swedish translation of the ETI exhibited similar psychometric properties as both the original version and translations.

    Paper III examined how childhood trauma and psychiatric comorbidity affect adult functioning - independently, through mediation or moderation. This was done in two samples consisting of 414 psychiatric outpatients and 100 non-clinical participants respectively. The study found that in clinical samples, both childhood trauma and comorbidity affected functioning, with comorbidity partially mediating the effect of trauma. In the non-clinical sample, only comorbidity was associated with functioning. No moderation effects were present in either sample.

    Paper IV explored predictors of functioning and their combined predictive power. Temperament and character traits, attachment styles, childhood trauma and psychiatric comorbidity including personality disorders were assessed in 137 psychiatric outpatients. While many variables individually predicted functioning, only the temperament trait Harm Avoidance and the character trait Self-Directedness remained significant predictors in a multiple regression analysis, explaining about one-third of the variance. These findings emphasize the role of personality traits in understanding and predicting the functioning of psychiatric patients.

    In summary, the studies in this thesis support that functioning and childhood trauma can be measured with good reliability using the SDS and ETISR-SF, and that personality factors may be important predictors of functioning in psychiatric patients.

    List of papers
    1. The Swedish version of the Sheehan Disability Scale – a valid and brief measure of functioning
    Open this publication in new window or tab >>The Swedish version of the Sheehan Disability Scale – a valid and brief measure of functioning
    2016 (English)In: European Journal of Person Centered Healthcare, ISSN 2052-5656, Vol. 4, no 1, p. 1-7Article in journal (Refereed) Published
    Abstract [en]

    Rationale, aims and objective: The Sheehan Disability Scale (SDS) is a brief instrument used to measure functional disability, but the Swedish translation has not been psychometrically evaluated. The aim of this paper is to test the psychometric properties of the Swedish translation and to further examine concurrent and external validity.

    Method: In this cross-sectional study, 160 young psychiatric patients from an open care unit in Sweden, were recruited based on a clinical diagnosis of Attention Deficit Hyperactivity Disorder (ADHD), Bipolar Disorder (BD) and/or Borderline Personality Disorder (BPD) and re-diagnosed for confirmation. Participants were interviewed concerning socio-demographic data and a socio-demographic index (SDI) was constructed. Reliability of SDS was measured as internal consistency and an exploratory factor analysis was performed. Level of functioning was measured by SDS scores and Global Assessment of Functioning (GAF). SDS, both self-assessed and expert rated and GAF scores were compared to measure concurrent validity, while SDS and the SDI were compared to measure external validity.

    Results: The Swedish SDS had a Cronbach’s alpha coefficient of 0.77. An exploratory factor analysis showed that the SDS-items loaded on a single factor with an eigenvalue of 2.06. Self-assessed SDS-scores correlated with expert rated GAF-scores (r = -0.606) and, to some extent, with SDI scores (r = 0.280). Patients with an SDI score ≥ 1 had higher SDS-scores (t=2.70, p=0.008).

    Conclusions: The Swedish SDS has similar psychometric properties as the English and Spanish versions. It showed both concurrent and external validity, but external validity was weaker

    Keywords
    Assessment of impairment, Attention Deficit Hyperactivity Disorder (ADHD), Bi-polar Disorder (BD), Borderline Personality Disorder (BPD), disability evaluation, person-centered healthcare, psychometric evaluation, psychometric properties, reliability
    National Category
    Psychiatry
    Identifiers
    urn:nbn:se:uu:diva-318539 (URN)10.5750/ejpch.v4i1.1075 (DOI)
    Available from: 2017-03-25 Created: 2017-03-25 Last updated: 2025-01-14Bibliographically approved
    2. Early Trauma Inventory Self-Report Short Form (ETISR-SF): validation of the Swedish translation in clinical and non-clinical samples.
    Open this publication in new window or tab >>Early Trauma Inventory Self-Report Short Form (ETISR-SF): validation of the Swedish translation in clinical and non-clinical samples.
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    2019 (English)In: Nordic Journal of Psychiatry, ISSN 0803-9488, E-ISSN 1502-4725, Vol. 73, no 2, p. 81-89Article in journal (Refereed) Published
    Abstract [en]

    PURPOSE: Childhood trauma in an important public health concern, and there is a need for brief and easily administered assessment tools. The Early Trauma Inventory (ETI) is one such instrument. The aim of this paper is to test the psychometric properties of the Swedish translation of the short, self-rated version (ETISR-SF), and to further validate the instrument.

    MATERIALS AND METHODS: In this cross-sectional study, 243 psychiatric patients from an open care unit in Sweden and 56 controls were recruited. Participants were interviewed and thereafter completed the ETISR-SF. Internal consistency was calculated using Cronbach's alpha, a confirmatory factor analysis (CFA) was performed and goodness-of-fit was determined. Intra Class Correlation (ICC) was used to calculate test-retest reliability. Discriminant validity between groups was gauged using the Mann-Whitney U-test.

    RESULTS: Cronbach's alpha varied between 0.55 and 0.76, with higher values in clinical samples than in controls. Of the four domains, general trauma showed a lower alpha than the other domains. The CFA confirmed the four-factor model previously seen and showed good to acceptable fit. The ICC value was 0.93, indicating good test-retest reliability. According to the Mann-Whitney U-test, the non-clinical sample differed significantly from the clinical sample, as did those with PTSD or borderline diagnosis from those without these diagnoses.

    CONCLUSIONS: The Swedish translation of the ETISR-SF was found to have similar psychometric properties as both the original version and translations. ETISR-SF scores could also distinguish between different diagnostic groups associated with various degrees of trauma, which supports its discriminant validity.

    Keywords
    Childhood trauma, ETI, Early Trauma Inventory, translation, validation
    National Category
    Psychiatry
    Identifiers
    urn:nbn:se:uu:diva-401789 (URN)10.1080/08039488.2018.1498127 (DOI)30900487 (PubMedID)
    Available from: 2020-01-08 Created: 2020-01-08 Last updated: 2024-12-12Bibliographically approved
    3. Exploring the role of childhood trauma and psychiatric comorbidity for adult level of functioning
    Open this publication in new window or tab >>Exploring the role of childhood trauma and psychiatric comorbidity for adult level of functioning
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Background:  Childhood trauma and psychiatric comorbidity are both associated with impaired functioning in adulthood, but the nature of the interplay between these two on adult functioning is poorly understood. The aim of this paper was to determine how childhood trauma and psychiatric comorbidity affect adult functioning: independently, through mediation or moderation.

    Methods:   Two samples were used in this cross-sectional study: 414 young adult clinical psychiatric outpatients and 100 non-clinical participants. Participants were diagnosed and completed self-rated measures of childhood traumatisation, Early Trauma Inventory, and of current functioning, Sheehan Disability Scale. Multiple regression analysis, mediation- and moderation modelling was used to explore the interplay between the variables. 

    Results: In the clinical sample, both childhood trauma and comorbidity were associated with functioning, and roughly one fourth of the effect of childhood trauma was mediated through comorbidity. There were no moderation effects. In the non-clinical sample, only comorbidity was associated with functioning, and no mediation or moderation effects were found. 

    Conclusions: Comorbidity has an effect on functioning in both groups, but childhood trauma had no effect on functioning in the non-clinical sample. In the clinical sample, there was a partial mediating effect through comorbidity, accounting for some of the association between childhood trauma and adult functioning. In both samples, trauma and comorbidity only accounted only for a small part of the variance in functioning, and further research on other factors affecting functioning is needed. 

    Keywords
    psykiatri, funktion, trauma, samsjuklighet
    National Category
    Psychiatry
    Research subject
    Medical Science
    Identifiers
    urn:nbn:se:uu:diva-545118 (URN)
    Available from: 2024-12-12 Created: 2024-12-12 Last updated: 2024-12-12
    4. Beyond Symptoms - A Cross-Sectional Study Exploring Functioning in Psychiatric Outpatients.
    Open this publication in new window or tab >>Beyond Symptoms - A Cross-Sectional Study Exploring Functioning in Psychiatric Outpatients.
    2024 (English)In: Psychiatry, ISSN 0033-2747, E-ISSN 1943-281X, Vol. 87, no 4, p. 353-371Article in journal (Refereed) Published
    Abstract [en]

    OBJECTIVE: This study aimed to explore factors influencing functioning in psychiatric outpatients, both separately and in combination. The primary objectives were to determine predictors of functioning, assess their significance in a combined analysis, and quantify their collective predictive power.

    METHOD: A sample of 137 psychiatric outpatients diagnosed with bipolar disorder, borderline personality disorder, or attention deficit hyperactivity disorder (ADHD) participated in this cross-sectional study, undergoing semi-structured diagnostic interviews for psychiatric and personality disorders. Participants also completed assessments of current functioning, personality traits (temperament and character), attachment style, and childhood trauma. Linear regression models were employed to analyse the relationships between these factors and level of functioning.

    RESULTS: The majority of temperament and character traits and attachment dimensions, as well as having a personality disorder, predicted impaired functioning, but comorbidity and childhood trauma did not. When all variables were taken into account in a multiple regression analysis, only the temperament and character traits Harm Avoidance and Self-directedness remained significantly predictive (p = .006 and .003, respectively). These two factors explain about one-third of the variance.

    CONCLUSIONS: Personality traits-more specifically, the temperament trait Harm Avoidance and the character trait Self-directedness-are strong predictors of functioning among psychiatric outpatients. Interestingly, when accounting for these factors, traditionally associated variables, such as attachment, comorbidity, and childhood trauma, lost their significance as predictors. These findings underscore the pivotal role of specific personality traits in understanding and predicting the functioning of psychiatric patients.

    National Category
    Clinical Medicine Psychiatry
    Identifiers
    urn:nbn:se:uu:diva-545114 (URN)10.1080/00332747.2024.2395754 (DOI)39258895 (PubMedID)
    Available from: 2024-12-12 Created: 2024-12-12 Last updated: 2024-12-12
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  • Public defence: 2025-02-25 13:40 Lecture hall Sonja Lyttkens, Uppsala
    Bånkestad, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control.
    Structured models for scientific machine learning: From graphs to kernels2025Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis investigates the reciprocal relationship between science and machine learning, showing how embedding scientific principles within machine learning models enhances accuracy and interpretability in complex scientific domains. Through five contributions, this work addresses challenges spanning molecular modeling, fluid dynamics, and graph-based learning, illustrating how scientific insights can guide model development and improve performance across diverse applications.

    A central focus is developing models that directly incorporate physical symmetries and laws into their structure, creating novel, scientifically grounded approaches. For instance, the GeqShift model leverages E(3)-equivariant graph neural networks to predict NMR spectra with a significant accuracy boost by capturing three-dimensional molecular structures. Similarly, our SE(2)-equivariant graph neural network models rotational and translational symmetries to enhance data efficiency and performance in fluid dynamics simulations, demonstrating the strength of symmetry-aware models in complex physical domains.

    This thesis advances graph-based machine learning by developing physics-informed models. For example, we introduce a subsampling model that incorporates principles from the classic Ising model of magnetism, introducing a novel approach to graph subsampling that enhances tasks like graph explanation and mesh sparsification. Building on these graph-based techniques, we also present an approach to nonnegative matrix factorization (NMF), leveraging graph structures to accelerate low-rank factorization.

    In addition to symmetry-aware frameworks, we introduce the elliptical process, a flexible extension of the Gaussian process that adapts to non-Gaussian noise. This innovation allows the model to learn noise characteristics directly from data, producing robust predictions that address a broad spectrum of real-world challenges. 

    These contributions underscore the dynamic exchange between scientific principles and machine learning, illustrating how physical knowledge enhances model performance and inspires new solutions. This thesis establishes a foundational framework for advancing scientific machine learning, paving the way for future breakthroughs in the field.

    List of papers
    1. Ising on the Graph: Task-specific Graph Subsampling via the Ising Model
    Open this publication in new window or tab >>Ising on the Graph: Task-specific Graph Subsampling via the Ising Model
    2024 (English)In: Proceedings of theThird Learning on Graphs Conference (LoG 2024), Proceedings of Machine Learning Research , 2024Conference paper, Published paper (Refereed)
    Abstract [en]

    Reducing a graph while preserving its overall properties is an important problem with many applications. Typically, reduction approaches either remove edges (sparsification) or merge nodes (coarsening) in an unsupervised way with no specific downstream task in mind. In this paper, we present an approach for subsampling graph structures using an Ising model defined on either the nodes or edges and learning the external magnetic field of the Ising model using a graph neural network. Our approach is task-specific as it can learn how to reduce a graph for a specific downstream task in an end-to-end fashion without requiring a differentiable loss function for the task. We showcase the versatility of our approach on four distinct applications: image segmentation, explainability for graph classification, 3D shape sparsification, and sparse approximate matrix inverse determination.

    Place, publisher, year, edition, pages
    Proceedings of Machine Learning Research, 2024
    Series
    Proceedings of Machine Learning Research, ISSN 2640-3498 ; 269
    National Category
    Computer Sciences
    Research subject
    Machine learning
    Identifiers
    urn:nbn:se:uu:diva-545653 (URN)
    Conference
    The Third Learning on Graphs Conference (LoG 2024), Virtual Event, November 26–29, 2024
    Available from: 2024-12-19 Created: 2024-12-19 Last updated: 2025-01-10Bibliographically approved
    2. Carbohydrate NMR chemical shift prediction by GeqShift employing E(3) equivariant graph neural networks
    Open this publication in new window or tab >>Carbohydrate NMR chemical shift prediction by GeqShift employing E(3) equivariant graph neural networks
    2024 (English)In: RSC Advances, E-ISSN 2046-2069, Vol. 14, no 36, p. 26585-26595Article in journal (Refereed) Published
    Abstract [en]

    Carbohydrates, vital components of biological systems, are well-known for their structural diversity. Nuclear Magnetic Resonance (NMR) spectroscopy plays a crucial role in understanding their intricate molecular arrangements and is essential in assessing and verifying the molecular structure of organic molecules. An important part of this process is to predict the NMR chemical shift from the molecular structure. This work introduces a novel approach that leverages E(3) equivariant graph neural networks to predict carbohydrate NMR spectral data. Notably, our model achieves a substantial reduction in mean absolute error, up to threefold, compared to traditional models that rely solely on two-dimensional molecular structure. Even with limited data, the model excels, highlighting its robustness and generalization capabilities. The model is dubbed GeqShift (geometric equivariant shift) and uses equivariant graph self-attention layers to learn about NMR chemical shifts, in particular since stereochemical arrangements in carbohydrate molecules are characteristics of their structures.

    Place, publisher, year, edition, pages
    Royal Society of Chemistry, 2024
    National Category
    Organic Chemistry Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-537764 (URN)10.1039/d4ra03428g (DOI)001296088100001 ()39175672 (PubMedID)
    Funder
    Swedish Research Council, 2022-03014Knut and Alice Wallenberg Foundation
    Available from: 2024-09-05 Created: 2024-09-05 Last updated: 2025-01-04Bibliographically approved
    3. Flexible SE (2) graph neural networks with applications to PDE surrogates
    Open this publication in new window or tab >>Flexible SE (2) graph neural networks with applications to PDE surrogates
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    This paper presents a novel approach for constructing graph neural networks equivariant to 2D rotations and translations and leveraging them as PDE surrogates on non-gridded domains. We show that aligning the representations with the principal axis allows us to sidestep many constraints while preserving SE(2) equivariance. By applying our model as a surrogate for fluid flow simulations and conducting thorough benchmarks against non-equivariant models, we demonstrate significant gains in terms of both data efficiency and accuracy.

    National Category
    Computer Sciences
    Research subject
    Scientific Computing; Computer Science; Computer Science
    Identifiers
    urn:nbn:se:uu:diva-546608 (URN)
    Available from: 2025-01-10 Created: 2025-01-10 Last updated: 2025-01-15
    4. Variational Elliptical Processes
    Open this publication in new window or tab >>Variational Elliptical Processes
    2023 (English)In: Transactions on Machine Learning Research, E-ISSN 2835-8856Article in journal (Refereed) Published
    Abstract [en]

    We present elliptical processes—a family of non-parametric probabilistic models that subsumes Gaussian processes and Student's t processes. This generalization includes a range of new heavy-tailed behaviors while retaining computational tractability. Elliptical processes are based on a representation of elliptical distributions as a continuous mixture of Gaussian distributions. We parameterize this mixture distribution as a spline normalizing flow, which we train using variational inference. The proposed form of the variational posterior enables a sparse variational elliptical process applicable to large-scale problems. We highlight advantages compared to Gaussian processes through regression and classification experiments. Elliptical processes can supersede Gaussian processes in several settings, including cases where the likelihood is non-Gaussian or when accurate tail modeling is essential.

    National Category
    Other Computer and Information Science
    Research subject
    Machine learning; Artificial Intelligence
    Identifiers
    urn:nbn:se:uu:diva-516855 (URN)
    Funder
    Wallenberg AI, Autonomous Systems and Software Program (WASP)Swedish Foundation for Strategic Research, SM19-0029Kjell and Marta Beijer FoundationKnut and Alice Wallenberg Foundation
    Available from: 2023-11-30 Created: 2023-11-30 Last updated: 2025-01-04Bibliographically approved
    5. Graph-based Neural Acceleration for Nonnegative Matrix Factorization
    Open this publication in new window or tab >>Graph-based Neural Acceleration for Nonnegative Matrix Factorization
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    We describe a graph-based neural acceleration technique for nonnegative matrix factorization that builds upon a connection between matrices and bipartite graphs that is well-known in certain fields, e.g., sparse linear algebra, but has not yet been exploited to design graph neural networks for matrix computations. We first consider low-rank factorization more broadly and propose a graph representation of the problem suited for graph neural networks. Then, we focus on the task of nonnegative matrix factorization and propose a graph neural network that interleaves bipartite self-attention layers with updates based on the alternating direction method of multipliers. Our empirical evaluation of synthetic and two real-world datasets shows that we attain substantial acceleration, even though we only train in an unsupervised fashion on smaller synthetic instances. 

    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-546606 (URN)
    Available from: 2025-01-10 Created: 2025-01-10 Last updated: 2025-01-15
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  • Public defence: 2025-02-26 10:00 Hambergsalen, Uppsala
    Thallam, Venugopal
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, LUVAL. Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Natural Resources and Sustainable Development, CEMUS Research Forum, CEFO.