Fysik // Physics
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Explores and uses physics to understand the world, and provide applications, new materials and innovations that meet today's needs, and the challenges of the future.
Stimulated by major needs and challenges in society and industry, our ambition is to foster a creative environment for academic research, learning, innovations and utilisation. We provide a competitive advantage by linking top-level international and interdisciplinary academic performance in the areas of material science, nanotechnology, life science engineering and energy research with world-leading industrial R&D&I projects.
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Browsar Fysik // Physics efter Program "Biomedical engineering (MPBME), MSc"
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- PostAssembly and disassembly of the influenza C matrix protein layer on a lipid membrane(2016) Eklund, Birger; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)Insight into the inner workings of viruses is an important piece of knowledge in humanity’s expanding collection of knowledge which can potentially be used to treat or prevent diseases. Influenza C is known to cause an infection with cold-like symptoms with possible complications in young children. The virus is a lipid-enveloped RNA virus in the Orthomyxoviridae family and incorporates 9 proteins. One of these is matrix protein 1 (M1C) which is found on the inside of the lipid-envelope of the virion. Influenza C in general and M1C in particular have not been extensively studied. However, influenza A and it’s matrix protein 1 have been studied to a great extent. In this thesis the binding and release of M1C on supported lipid bilayers (SLB) in various environments have been investigated. The SLB is a basic model of the lipid envelope of the influenza virions which is also suitable for the two surfacebased techniques used in this work. The two main environmental factors that were varied were the salinity and pH of the surrounding solution. The protein-protein and protein-bilayer binding behaviours were the two main interactions examined. In the Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) the amount of M1C bound to an SLB was measured. Information on the adlayer’s viscoelastic properties was also obtained. With this technique it was revealed that the binding of the protein is highly dependent on electrostatic charges. In the microscope, fluorescence and Surface Enhanced Ellipsometric Contrast (SEEC) microscopy was used to observe the spatial arrangement of the M1C on the SLB. The SEEC microscopy was used to observe aggregations of M1C on the SLB. A fraction of the negatively charged lipids in the SLB were tagged with the fluorescent dye NBD and the clustering of these was observed with fluorescence microscopy. This combined with the SEEC observations gave the conclusion that the proteins aggregate on the SLB and recruit negatively charged lipids. This work found that the main binding strategy for M1C is is to utilise electrostatic forces. This is important because this binding is used both in the forming of the virions and for maintaining the structural integrity of the virion. It was also found that endosomal pH leads to some dissociation of M1C from the lipid bilayer. This is important since the dissolution of the virion’s matrix protein layer in the endosome has been shown to be vital for infection in influenza A.
- PostBrachycephalic Obstructive Airway Syndrome (BOAS) classification in dogs based on respiratory noise analysis using machine learning(2021) Mårtensson, Moa; Chalmers tekniska högskola / Institutionen för fysik; Karlsteen, Magnus; Karlsteen, Magnus; Skiöldebrand, EvaBrachycephalic Obstructive Airway Syndrome (BOAS) is a problem in several dog breeds due to a compressed shape of the skull. It is classified as BOAS grade 0-3, where 0 is normal breathing and 3 is the most severe grade of the syndrome. Grade 2-3 can cause great suffering for the affected dogs and needs treatment. This study aimed to find a method using machine learning to classify the BOAS grade based on audio recordings of respiratory noise. The recordings were converted into Mel-Frequency Cepstral Coefficients (MFCCs) to be processed as images by the network. The results proved that Recurrent Neural Network - Long Short-Term Memory (RNN-LSTM) was a successful method to classify the four different BOAS grades with an accuracy of about 86-87% for dictaphone recordings and about 62-66% for stethoscope recordings. Convolutional Neural Networks (CNN) also managed to classify the BOAS grades but this method was less accurate, with an accuracy of approximately 74-76% for dictaphone recordings and 50-54% for stethoscope recordings. The study was a collaboration between Chalmers University of Technology and Swedish University of Agricultural Sciences.
- PostCell Topography Correction in Colocalization Analysis(2022) Almehed, Sara; Chalmers tekniska högskola / Institutionen för fysik; Höök, Fredrik; Parmryd, IngelaColocalization analysis is the study of the distributions of species with fluorescence microscopy. By estimating the spatial distribution of the fluoresence emission from two types of molecules, colocalization analysis is used as a method to help in the understanding of processes and interactions between molecules both within cells and with their environment. One of the basic assumptions of colocalization analysis today is that the species of interest are spatially distributed on a uniform surface, their only interaction being with each other. The assumption of a uniform surface however, does not always hold. The plasma membrane for example, is not flat but can be convoluted, folded and deformed in a large number of ways, causing the assumption of a flat surface to not be applicable when studying molecules present in the membrane of a cell. With aim to improve the result of colocalization analysis, we present a method of intensity normalization by weighting the observed intensities of the species of interest by the membrane distribution. To study the effect of background normalization on colocalization analysis, simulations were conducted on non-uniform surfaces where the Pearson correlation coefficient and Spearman rank correlation coefficient were used to estimate the amount of colocalization before and after background normalization. Based on the simulations, together with results from analysis of experimental images using confocal laser scanning microscopy, we present a proof of concept for the effect of background normalization on colocalization analysis.
- PostCharacterization of Lipopolysaccharide -containing supported lipid bilayers(2016) Börjesson, Per; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)Bacteria have played a huge role over the course of human history. Some bacterial strains have wrought havoc and others have proved hugely beneficial and exist in a symbiotic relationship with humans. Regardless of the type of bacteria, a better understanding of how they communicate and interact with their environment is of great value, for example when developing new types of drugs targeting bacteria. However, the complexity of bacterial membranes and the myriad of surface active molecules and proteins found on it, makes the analysis of specific biomolecular interactions occurring at bacterial membranes a challenging task. This project has therefore focused on developing sensing platforms. The first sensing platform mimics bacterial surfaces by presenting specific biomolecules in a native but wellcontrolled manner. It therefore comes in the form of a supported lipid bilayer (SLB) consisting of mainly 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and lipopolysaccharides (LPS). The second approach used in this thesis was to extract native membranes directly from bacteria and use these to form an SLB. The SLBs were characterized in order to verify their composition, as well as to determine their physiochemical properties and biological activity. The potential platform was also demonstrated in binding experiments using the LPS-binding molecule human lactoferrin. The outcome was analyzed using quartz crystal microbalance with dissipation monitoring (QCM-D) or total internal reflection microscopy (TIRFM). It was determined that LPS have successfully been incorporated into the SLB and that vesicles created using native membranes extracted from bacteria could also be used to form SLBs. It was also determined that these sensing platforms could be used to study a variety of biomolecular interactions involving LPS.
- PostDirect feedback application for training with Osteoarthritis affected to the lower extremities(2021) Carlberg, Emelie; Chalmers tekniska högskola / Institutionen för fysik; Karlsteen, Magnus; Karlsteen, MagnusThis master’s thesis covers the development of an application for patients and healthcare providers training to alleviate Osteoarthritis symptoms. The method used in this application to judge if the training is performed in a safe and correct manner is by using angles. These angles are measured using the smartphone accelerometers, magnetometer and gyroscope. These signals are used to provide direct feedback to the user, using Euler angles and a complementary filter. The results indicate that the smartphone application can measure the angles of interest with good precision. There is still need for further development due to the problems of gimbal locking using Euler angles. Conclusions from the work is that there is great potential using the application both from a patient perspective and as a long term method for healthcare providers to follow up without physical visits.
- PostGait phase identification of various horse gaits using both wearable and video-based technologies(2022) Elander, Rebecka; Chalmers tekniska högskola / Institutionen för fysik; Karlsteen, Magnus; Karlsteen, Magnus; Siddhartha, Khandelwal; Roepstorff, LarsHealthy gait consists of locomotion, balance and the ability to adapt to the environment. The human gait cycle has been studied thoroughly and gait analysis has been used for various applications. The biomechanics of the horse is well-known, but there is a need to develop systems that can quantify the quality of equine gait, especially in the real world. Inertial Measurement Units (IMU’s) are small, lightweight, and ambulant sensors which can determine the position and orientation of the body segments they have been placed on. The aim of this study was to investigate the possibility of using an Inertial Measurement Unit (IMU) System, especially placed at the cannons, to identify the gait phases for walk and trot, and to use an Optical Motion Capture System to validate these with information from wearable sensors. The positions of the hooves and cannons were tracked using Qualisys Track Manager. The resultant acceleration of each position was calculated. The resultant acceleration of Movebeat’s acceleration data, was computed in each sample. Hoof Strikes and Toe Offs were detected using Tracker from video recordings from Qualisys. The acceleration patterns were similar for Movebeat and Qualisys for both hooves and cannons and the acceleration peaks almost coincided with Hoof Strike and Toe Off. However, there were some parts of the pattern that differed, where one probable explanation could be that the acceleration from Qualisys was estimated, while the acceleration from Movebeat was measured. The conclusions are that IMU’s placed on the cannons are able to identify the gait events for walk and trot with accuracy, and that Hoof Strike and Toe Off almost coincides with the acceleration peaks. However, further investigations of the accelerations and the gyros in the different directions, x, y and z, need to be done to simplify the identification of the gait phases. More studies need to be performed to further validate the consistency of the identifications. This study was a collaboration project between Chalmers University of Technology, Swedish University of Agricultural Sciences, and VectorizeMove AB.
- PostIntensity Modulated Proton Therapy for Hepatocellular Carcinoma(2017) Gotby Westlund, Lovisa; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)This is a preliminary study investigating the advantages and drawbacks of using intensity modulated proton therapy (IMPT) in the treatment of hepatocellular carcinoma (HCC) and compares this treatment modality with photon stereotactic body radiation therapy (SBRT). One patient, previously treated with photon SBRT, has been replanned and by benefiting from the protons finite range and the fact that most of the dose is deposited in the Bragg peak, proton treatment plans which efficiently spare the organs-at-risk (OARs) have been generated. The challenge with using IMPT when treating HCC however, is that the tumor moves over time due to breathing and the sensitive spatio-temporal resolution of the IMPT is therefore compromised in the treatment delivery, giving rise to the so-called interplay effect. This effect can be mitigated by, for example, breath hold, beam gating, tumor tracking or rescanning. The impact of interplay effect has been simulated for treatment delivery in breath hold as well as for free-breathing and the benefit of using rescanning has been investigated. All IMPT plans have superior tumor coverage in comparison with the photon SBRT plan, at the same time as having better OAR sparing. The dose delivery simulations show promising results for future clinical applications of robust proton therapy treatment plans for both delivery techniques, the trade-off between dose delivery in breath hold and freebreathing being treatment time versus sparing of OARs. However, more patient cases are needed in order to draw more general conclusions.
- PostPartial spider silk as scaffold for tissue engineering the aortic valve(2016) Tasiopoulos, Christos- Panagiotis; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)The aortic valve constitutes a complex tissue that has to unobtrusively operate in a continuous mode, in order to sufficiently supply the systemic circulation with oxygenated blood. Severe aortic valve diseases though result in a tissue function no longer competent to meet the innately demanding biomechanical criteria. Conventional treatment approaches may temporarily alleviate symptomatic patients nonetheless have long been associated with great limitations. Tissue engineering holds great promise to cope with drawbacks of to date status in diseased aortic valve treatment, although has not been fully explored yet. Recombinantly synthesized spider silk has undoubtedly opened a wide range of application areas where sound mechanical properties are required and hence, it might be considered an ideal aortic valve scaffold. In this study, partial spider silk utilized to coat surfaces as well as configured into 3D matrices was extensively evaluated in terms of cell adherence, proliferation, and tissue-specific protein secretion. To provide comparable information, cell-seeded protein coatings and 3D constructs in the forms of foam and fiber were also exposed to vigorous fluid dynamics. Results indicated profound cell compliance with host material in general but most importantly, significant cell growth in the dynamically conditioned fibroblasts and endothelial cells inside the silk variants. In addition, protein-coated substrates and fabricated scaffolds subjected to shear stresses were interestingly shown to facilitate protein synthesis by seeded cells in a higher degree. In conclusion, recombinantly synthesized spider silk can be considerably included in future tissue engineering the aortic valve studies.
- PostSkeletal Muscle Differentiation in 3D Capillary Gels(2016) klose, felix; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)Skeletal muscle tissue contributes to many functions in the human body such as locomotion and maintaining the body temperature. Tissue engineering could open up possibilities of grafting muscle tissue ex vivo and make way for new autologous treatments mitigating pathological muscle loss. Additionally, skeletal muscle tissue of mammal origin is one of the main nutritional protein sources in the western diet. Also here the production of skeletal muscle tissue ex vivo could provide measures to reduce environmental strains due to conventional live-stock production and produce food in a more resource efficient manner. Until a market maturity is achieved, methods have to be found to produce cells in high enough numbers and the differentiation has to be ensured to allow for functional tissue for medical applications and nutritionally valuable food. Additionally, the production of larger tissue-engineered constructs is challenging due to the absence of a perfusion network bringing the nutrients and oxygen deep into the constructs. The aim of the project is to grow parallel aligned muscle fibres in a three dimensional scaffold with the help of a perfusion bioreactor. The approach was to grow and differentiate C2C12 mouse myogenic progenitor cells inside capillary alginate gels. It was hypothesized that the parallel aligned capillary structure inside the gels could help the alignment of the muscle fibres and prospectively be used in generating muscle constructs closer to physiological muscle found in mammals. In order to promote cell attachment to the gels, different modifications of the alginate gel have been performed. Bulk modifications have been achieved by mixing pure alginate solutions with pre-coupled RGD-alginate or gelatin solutions prior to crosslinking. Furthermore, surface modifications have been performed via collagen coatings or carbodiimide coupling of RGD peptides to the surfaces of crosslinked alginate gels. Cell cultures were performed on the surface of samples cut from these gels to evaluate the attachment improvement of the various modifications and to study the influences of the capillaries on alignment of the cells. In addition to the cultures the scaffolds have been investigated by light and confocal microscopy. For three dimensional cell cultures a perfusion bioreactor has been designed. Computer-based simulations have been performed for in silica evaluations of the flow and oxygen distribution inside the bioreactor and the capillaries of the alginate gels. Eventually, the bioreactor and the RGD:alginate bulk modified gels were combined in 3D culture experiments to characterize the culture setup in different operational modes, to formulate protocols and to test the feasibility of the experimental setup for cell growth and differentiation. As a result of this project, a bioreactor system has been developed allowing for future investigations of capillary alginate gels as a culturing scaffold for skeletal muscle progenitor cells. The bulk modification with RGD-alginate seems to be most beneficial in growing high cell numbers and achieving good attachment quality of the cells to the alginate gels. Optimization of the sterilization techniques in concert with improved modifications of the alginate scaffold to better present the functional groups to the cells could lead to more promising results of the cell cultures. CaCl2 is recommended to be replaced by another crosslinking agent because the gels crosslinked with Ca2+ do not have the necessary structural integrity throughout the cell culture. A switch to covalently bound gels and more careful tailoring of the scaffold properties, e.g. elastic modulus, stress relaxation behaviour, could improve the outcome of the cell cultures. This project serves as a basis for future advancements in culturing skeletal muscle cells in vitro for nutritional as well as medical applications.
- PostStudy of bone anisotropy in porous metal lic implants using birefringence and X ray scattering imaging(2022) Björk, Ludvig; Chalmers tekniska högskola / Institutionen för fysik; Chalmers University of Technology / Department of Physics; Liebi, Marianne; Rodriguez Palomo , AdrianMetallic implants are commonplace in orthopaedic surgery. Recent advances in manufacturing technology have made it possible to manufacture 3D printed porous implants. This allows for designs that are mechanically tailored to fit their envi ronment. Bone growth in porous implants has been previously investigated, how ever this thesis studies the anisotropy of bone surrounding porous and non-porous metallic implants through imaging methods such as birefringence microscopy and small-angle X-ray scattering (SAXS). Data from birefringence microscopy is corrected using Mueller calculus and the fast axis angle and retardance of bone is analysed. As the region of interest is too large for the microscope field of view, four images are stitched using the scale-invariant fea ture transform and random sample consensus algorithms. The birefringence data is validated through correlation with SAXS experiments. Additionally, 3D reconstruc tion of SAXS data is performed using real unrestricted spherical harmonic tensor tomography. The validation of birefringence data indicates that the source of birefringence in bone is from collagen fibres. As a result, birefringence microscopy is used to show that fibres outside the area affected by implantation have a preferred orientation along the longitudinal axis and fibres inside of the porous implant have a preferred orientation that correlate with the geometry of the implant. Moreover, around the perimeter of the implant, bone growth is disordered as some fibres wrap around the outside of the implant, and some grow into pores. This shows that the geometry of the implant plays an important role in the anisotropy of bone, which can efficiently be studied using birefringence microscopy and SAXS
- PostThree aspects of neural signalling with focus on pain – propagation, inhibition and application(2011) Mona, Johansson; Chalmers tekniska högskola / Institutionen för teknisk fysik; Chalmers University of Technology / Department of Applied PhysicsThis thesis includes three different aspects of neural signalling, a new mathematical model for the action potential and its propagation, an experiment of how general anaesthetic affect the membrane of a neuron and speculations about what mechanisms underlie pain relief of the bioelectric dressing; ProcelleraTM . At present the mathematical models for an action potential and its propagation is based on Hodgkin & Huxley´s model which is heavily founded on experimental result and consists of a very complex expression. This thesis present a new model which is based on the observed phenomenon that the axon is expanded when the action potential is transferred, this results in a much simpler expression. These equations are also visualized through simulations in finite element method based programme, COMSOLTM and show the same behaviour as an action potential, i.e. a pulse shape. The essential feature of general anaesthetic is that it inhibits neural signals. How it does this is debated in the scientific community. Different field of science provides different explanations. There is a well known rule; the Meyer-Overton rule which says that the effect of general anaesthetic is proportional to its solubility in olive oil which resembles the axon membrane. This thesis presents experiments where QCM-D (Quartz Crystal Microbalance with Dissipation monitoring) is used to observe how the resonance frequency and dissipation of a membrane is change when general anaesthetic is dissolved in it. It also present an experiment monitoring the electrical properties changes of the membrane due to general anaesthetic. The bioelectric dressing ProcelleraTM is at present claimed to reduce the pain sensation in a wound, by inhibition of the pain signal. The dressing contains zinc and silver elements and therefore this thesis speculates in how these metals can result in pain reduction. This speculation discuss different receptors inhibition, chemical reactions and other mechanisms which are possible to occur in the interaction of the dressing and the wound.
- PostUsing fibrinogen barriers to restrict the motion of shear-driven supported lipid bilayers(2011) Olsson, Thomas; Chalmers tekniska högskola / Institutionen för teknisk fysik; Chalmers University of Technology / Department of Applied PhysicsAbout 70% of all drug targets are proteins situated in the cell-membrane. However, the cellmembrane offers a very complex environment in which to study just a single type of interaction with a specific type of protein, being made up of hundreds of different lipids, over 200 different proteins and oligosaccharides. There exist for this reason some different simplified models of cell membranes, where only the base of the cell-membrane is used, a bilayer often made up of just one type of lipids. A certain protein could then be incorporated into the lipid bilayer and be studied. One simplified model of the cell-membrane is a supported lipid bilayer, which is a lipid bilayer formed on a solid support. SLBs, which is the model used in this work, are formed in microfluidic channels, due to the high level of controllability it offers with laminar flows, but also requiring only small quantities of samples. It was shown by Jönsson et. al that an SLB could be made to move in a desired direction in the microfluidic channel, by having a relatively high bulk flow in the channel above the formed SLB. This proved very useful as molecules incorporated into an SLB was shown to accumulate at the front of the moving bilayer, an increasing concentration of for example a certain protein to be studied means an increase in signal strength. An increase in signal strength could for example mean that things could be studied which would otherwise drown in noise due to too low concentrations. A microfluidic channel is made of glass and PDMS, both materials on which SLBs can form. This means that an SLB when moving along the channel floor could also start moving up along the walls of the channels, thus taking with it incorporated molecules which could have been accumulated at the front. In a microfluidic channel the flow profile is such that bulk flow velocity is highest in the middle of the channel and goes down to zero at the walls, this reduce the effectiveness of the accumulation as some accumulated molecules close to the walls are continuously left behind. Fibrinogen is a protein which with the right conditions could be made to adsorb densely on the channel surface. When fibrinogen is densely packed, it forms a barrier stable enough to restrict the motion of a moving SLB. Fibrinogen barriers are studied within this work as a means of constricting the moving SLB to the center of the microfluidic channel in order to stop it from moving up the channel walls and also to increase the effectiveness of the accumulation as the zero bulk flow regions are avoided. Some results from this study are that fibrinogen indeed can form a barrier dense enough to withstand a moving bilayer, and that accumulation at the front is more effective when fibrinogen barriers are used.
- PostWinning the Race: Bacterial Growth versus Dynamic Dosage of Antimicrobial Compounds(2017) Mahr, Daniel; Chalmers tekniska högskola / Institutionen för fysik (Chalmers); Chalmers University of Technology / Department of Physics (Chalmers)Great pain and suffering to patients as well as high financial burden to health care systems are caused by chronic wounds. The interrupted wound healing mechanism is often due to increased bacterial load, whereof conventional treatment via antibiotics is affected by a recent increase in developing multiple antibiotic resistances. This suggests alternative treatments like wound dressings that release antimicrobial substances. A model for dynamic dosage of the antiseptic compound polyhexamethylene biguanide (PHMB) was introduced to investigate the time-kill behaviour of Gram-negative Pseudomonas aeruginosa and Gram-positive Staphylococcus aureus. This was hypothesised to allow findings about dependences on pharmacodynamic and pharmacokinetic parameters. Such knowledge might grant conclusions about necessary release kinetics of PHMB in wound dressings. Four different concentration profiles of PHMB were used, starting at 0 μM and then reaching the respective minimum inhibitory concentration (MIC) against bacteria after 3, 6, 9, and 24 h by linear increase. Bacteria were cultured in these concentration profiles for 48 h and regular viable count was performed. Reaching the MIC of PHMB after 3 h resulted in killing Pseudomonas aeruginosa, reaching it after 6 h showed inhibited growth and reaching it after 9 h or later showed no effect. Staphylococcus aureus still were killed by reaching the MIC of PHMB after 6 h, whereas reaching it after 9 h showed inhibited growth only. Reaching it later did not affect bacterial growth. After 48 h of culturing, all populations recovered to stationary growth phase. PHMB seemed to be more potent against Gram-positive Staphylococcus aureus. Conclusions about pharmacodynamic and pharacokinetic parameters of the effect of PHMB on bacteria were impeded as only a series of increasing, but no decreasing concentration gradients was tested. However, a greater effect during higher initial concentrations suggests dependence on the maximum concentration and on the time until the MIC is reached. Despite the necessity of further research that includes for instance a later decrease in concentration of PHMB, these early results suggest PHMB in wound dressings to be released as fast as possible and in a determined bactericidal dosage after application to the wound in order to act with highest efficacy of bacteria toxicity.