| 1. |
- Alakpa, Enateri V., et al.
(författare)
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Bioprinted schwann and mesenchymal stem cell co-cultures for enhanced spatial control of neurite outgrowth
- 2023
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Ingår i: Gels. - : MDPI. - 2310-2861. ; 9:3
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Tidskriftsartikel (refereegranskat)abstract
- Bioprinting nerve conduits supplemented with glial or stem cells is a promising approach to promote axonal regeneration in the injured nervous system. In this study, we examined the effects of different compositions of bioprinted fibrin hydrogels supplemented with Schwann cells and mesenchymal stem cells (MSCs) on cell viability, production of neurotrophic factors, and neurite outgrowth from adult sensory neurons. To reduce cell damage during bioprinting, we analyzed and optimized the shear stress magnitude and exposure time. The results demonstrated that fibrin hydrogel made from 9 mg/mL of fibrinogen and 50IE/mL of thrombin maintained the gel’s highest stability and cell viability. Gene transcription levels for neurotrophic factors were significantly higher in cultures containing Schwann cells. However, the amount of the secreted neurotrophic factors was similar in all co-cultures with the different ratios of Schwann cells and MSCs. By testing various co-culture combinations, we found that the number of Schwann cells can feasibly be reduced by half and still stimulate guided neurite outgrowth in a 3D-printed fibrin matrix. This study demonstrates that bioprinting can be used to develop nerve conduits with optimized cell compositions to guide axonal regeneration.
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| 2. |
- Castelain, Mickaël, et al.
(författare)
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Characterization of the Biomechanical Properties of T4 Pili Expressed by Streptococcus pneumoniae – A Comparison between Helix-like and Open Coil-like Pili
- 2009
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Ingår i: ChemPhysChem. - : Wiley. - 1439-4235 .- 1439-7641. ; 10:9-10, s. 1533-1540
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial adhesion organelles, known as fimbria or pili, are expressed by Gram–positive as well as Gram–negative bacteria families. These appendages play a key role in the first steps of the invasion and infection processes, and they therefore provide bacteria with pathogenic abilities. To improve the knowledge of pili-mediated bacterial adhesion to host cells and how these pili behave under the presence of an external force, we first characterize, using force measuring optical tweezers, open coil-like T4 pili expressed by Gram–positive Streptococcus pneumoniae with respect to their biomechanicalproperties. It is shown that their elongation behavior can be well described by the worm-like chain model and that they possess a large degree of flexibility. Their properties are then compared with those of helix-like pili expressed by Gram–negative uropathogenic Escherichia coli (UPEC), which have different pili architecture. The differences suggest that these two types of pili have distinctly dissimilar mechanisms to adhere and sustain external forces. Helix-like pili expressed by UPEC bacteria adhere to host cells by single adhesins located at the distal end of the pili while their helix-like structures act as shock absorbers to dampen the irregularly shear forces induced by urine flow and to increase the cooperativity of the pili ensemble. Open coil-like pili expressed by S. pneumoniae adhere to cells by a multitude of adhesins distributed along the pili. It is hypothesized that these two types of pili represent different strategies of adhering to host cells in the presence of external forces. When exposed to significant forces, bacteria expressing helix-like pili remain attached bydistributing the external force among a multitude of pili, whereas bacteria expressing open coil-like pili sustain large forces primarily by their multitude of binding adhesins.
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| 3. |
- Dahlberg, Tobias, et al.
(författare)
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3D printed water-soluble scaffolds for rapid production of PDMS micro-fluidic flow chambers
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We report a novel method for fabrication of three-dimensional (3D) biocompatible micro-fluidic flow chambers in polydimethylsiloxane (PDMS) by 3D-printing water-soluble polyvinyl alcohol (PVA) filaments as master scaffolds. The scaffolds are first embedded in the PDMS and later residue-free dissolved in water leaving an inscription of the scaffolds in the hardened PDMS. We demonstrate the strength of our method using a regular, cheap 3D printer, and evaluate the inscription process and the channels micro-fluidic properties using image analysis and digital holographic microscopy. Furthermore, we provide a protocol that allows for direct printing on coverslips and we show that flow chambers with a channel cross section down to 40 x 300 μm can be realized within 60 min. These flow channels are perfectly transparent, biocompatible and can be used for microscopic applications without further treatment. Our proposed protocols facilitate an easy, fast and adaptable production of micro-fluidic channel designs that are cost-effective, do not require specialized training and can be used for a variety of cell and bacterial assays. To help readers reproduce our micro-fluidic devices, we provide: full preparation protocols, 3D-printing CAD files for channel scaffolds and our custom-made molding device, 3D printer build-plate leveling instructions, and G-code.
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| 4. |
- Dahlberg, Tobias, 1990-
(författare)
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KNOW YOUR ENEMY : Characterizing Pathogenic Biomaterials Using Laser Tweezers
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Diseases caused by pathogenic agents such as bacteria and viruses result in devastating costs on personal and societal levels. However, it is not just the emergence of new diseases that is problematic. Antibiotic resistance among bacteria makes uncomplicated infections difficult and lethal. Resilient disease-causing spores spread in hospitals, the food industry, and water supplies requiring effective detection and disinfection methods. Further, we face complex neurological diseases where no effective treatment or diagnostic methods exist. Thus, we must increase our fundamental understanding of these diseases to develop effective diagnostic, detection, disinfection, and treatment methods.Classically, the methods used for detecting and studying the underlying mechanics of pathogenic agents work on a large scale, measuring the average macroscopic behavior and properties of these pathogens. However, just as with humans, the average behavior is not always representative of individual behavior. Therefore, it is also essential to investigate the characteristics of these pathogens on a single cell or particle level. This thesis develops and applies optical techniques to characterize pathogenic biomaterial on a single cell or particle level. At the heart of all these studies is our Optical Tweezers (OT) instrument. OT are a tool that allows us to reach into the microscopic world and interact with it. Finally, by combining OT with other experimental techniques, we can chemically characterize biomaterials and develop assays that mimic different biological settings. Using these tools, we investigate bacterial adhesion, disinfection, and detection of pathogenic spores and proteins.Hopefully, the insights of these studies can lessen the burden on society caused by diseases by helping others develop effective treatment, diagnostic, detection, and disinfection methods in the future.
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| 5. |
- Hanqing, Zhang, et al.
(författare)
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A fast and robust circle detection method using isosceles triangles sampling
- 2016
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Ingår i: Pattern Recognition. - : Elsevier. - 0031-3203 .- 1873-5142. ; 54, s. 218-228
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Tidskriftsartikel (refereegranskat)abstract
- Circle detection using randomized sampling has been developed in recent years to reduce computational intensity. However, randomized sampling is sensitive to noise that can lead to reduced accuracy and false-positive candidates. To improve on the robustness of randomized circle detection under noisy conditions this paper presents a new methodology for circle detection based upon randomized isosceles triangles sampling. It is shown that the geometrical property of isosceles triangles provides a robust criterion to find relevant edge pixels which, in turn, offers an efficient means to estimate the centers and radii of circles. For best efficiency, the estimated results given by the sampling from individual connected components of the edge map were analyzed using a simple clustering approach. To further improve on the accuracy we applied a two-step refinement process using chords and linear error compensation with gradient information of the edge pixels. Extensive experiments using both synthetic and real images have been performed. The results are compared to leading state-of-the-art algorithms and it is shown that the proposed methodology has a number of advantages: it is efficient in finding circles with a low number of iterations, it has high rejection rate of false-positive circle candidates, and it has high robustness against noise. All this makes it adaptive and useful in many vision applications.
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| 6. |
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| 7. |
- Larsson, Jonas, et al.
(författare)
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A hamiltonian derivation of interaction equations for Rossby waves
- 1999
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Ingår i: Physica scripta. T. - 0281-1847. ; T82, s. 71-73
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Tidskriftsartikel (refereegranskat)abstract
- The mode coupling equations for Rossby waves in a bounded periodic channel are derived by means of a Hamiltonian method. The streamfunction is used as field variable and we need not introduce Clebsch potentials or a lagrangian description. The Manley-Rowe relations follow from general hamiltonian theory.
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| 8. |
- Lindberg, Ann-Sofie, et al.
(författare)
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Firefighters' fit for duty score-model : Book of Abstracts
- 2016
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Ingår i: 21st Annual Congress of the European College of Sport Science: Crossing borders through sport science. - : ECSS.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Physical capacity has previously been deemed important for firefighters’ physical work capacity, and evaluation of fitness for duty is common in the pre-hiring process. Various methods have been used to establish cut-off limits, i.e. normative data or expert judges. In accordance with government regulation, both full-time and part-time firefighters in Sweden have to pass a medical examination and a test of physical work capacity for permission to execute smoke diving. The physical work capacity test is a pass or fail test: dressed in firefighting protective clothes and breathing apparatus (total weight 24 ± 0.5 kg), six minutes walking with the incline at 8 degrees and treadmill speed of 4.5 km/h is performed. Inclusion of additional physical tests and appropriate cut-off limits is a decision taken by each individual municipality. The aim of the present study was to create a score model for evaluation of fitness for duty in the pre-hiring process of firefighters. Methods A total of 128 (64 men and 64 women) subjects: full-time firefighters, part-time firefighters and civilians, were included. Subjects performed five simulated firefighting work tasks and a selected battery six of physical tests including; 500 m rowing, grip strength, endurance bench press, track running 3000 m, standing broadjump and upright barbell row. The combined information from subjective evaluated cut-off limits, breakpoint estimation, checkpoint estimation and percentiles were used to create a score-model MO-PM30 Performance: Mixed Session 424 21ST ANNUAL CONGRESS OF THE EUROPEAN COLLEGE OF SPORT SCIENCE for evaluation of fit for duty. Results The models yielded various cut-off limits on the same physical test, depending on the work task investigated, but all tests were scored on a 1-11 scale. Consequently, the maximum total score was 66 and the minimum total score was 6. The recommended minimum total score of six tests is 36. Discussion In this study we created a score-model for evaluation of firefighters’ fit for duty in the pre-hiring process. When pre-hiring physical tests are performed, an easily conducted battery of physical tests is important in order to reduce costs but still maintain high validity and reliability. The score-model is easy to understand, performance gives the same score irrespectively of age and sex and makes it possible for the aspirants to prepare for the included physical tests. Since a specific physical test differs in importance in the prediction of simulated work task performance, the lack of performance in one physical test may not be fully compensated with a higher performance in another physical test. Simplifying and generalizing a method makes it practically usable at the detriment of accuracy on an individual level.
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| 9. |
- Malyshev, Dmitry, et al.
(författare)
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Laser induced degradation of bacterial spores during micro-Raman spectroscopy
- 2022
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Ingår i: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy. - : Elsevier. - 1386-1425 .- 1873-3557. ; 265
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Tidskriftsartikel (refereegranskat)abstract
- Micro-Raman spectroscopy combined with optical tweezers is a powerful method to analyze how the biochemical composition and molecular structures of individual biological objects change with time. In this work we investigate laser induced effects in the trapped object. Bacillus thuringiensis spores, which are robust organisms known for their resilience to light, heat, and chemicals are used for this study. We trap spores and monitor the Raman peak from CaDPA (calcium dipicolinic acid), which is a chemical protecting the spore core. We see a correlation between the amount of laser power used in the trap and the release of CaDPA from the spore. At a laser power of 5 mW, the CaDPA from spores in water suspension remain intact over the 90 min experiment, however, at higher laser powers an induced effect could be observed. SEM images of laser exposed spores (after loss of CaDPA Raman peak was confirmed) show a notable alteration of the spores' structure. Our Raman data indicates that the median dose exposure to lose the CaDPA peak was ∼60 J at 808 nm. For decontaminated/deactivated spores, i.e., treated in sodium hypochlorite or peracetic acid solutions, the sensitivity on laser power is even more pronounced and different behavior could be observed on spores treated by the two chemicals. Importantly, the observed effect is most likely photochemical since the increase of the spore temperature is in the order of 0.1 K as suggested by our numerical multiphysics model. Our results show that care must be taken when using micro-Raman spectroscopy on biological objects since photoinduced effects may substantially affect the results.
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| 10. |
- Malyshev, Dmitry, et al.
(författare)
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Mode of action of Disinfection chemicals on the bacterial spore structure and their Raman spectra
- 2021
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Ingår i: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 93:6, s. 3146-3153
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Tidskriftsartikel (refereegranskat)abstract
- Contamination of toxic spore-forming bacteria is problematic since spores can survive a plethora of disinfection chemicals and it is hard to rapidly detect if the disinfection chemical has inactivated the spores. Thus, robust decontamination strategies and reliable detection methods to identify dead from viable spores are critical. In this work, we investigate the chemical changes of Bacillus thuringiensis spores treated with sporicidal agents such as chlorine dioxide, peracetic acid, and sodium hypochlorite using laser tweezers Raman spectroscopy. We also image treated spores using SEM and TEM to verify if we can correlate structural changes in the spores with changes to their Raman spectra. We found that over 30 min, chlorine dioxide did not change the Raman spectrum or the spore structure, peracetic acid showed a time-dependent decrease in the characteristic DNA/DPA peaks and ∼20% of the spores were degraded and collapsed, and spores treated with sodium hypochlorite showed an abrupt drop in DNA and DPA peaks within 20 min and some structural damage to the exosporium. Structural changes appeared in spores after 10 min, compared to the inactivation time of the spores, which is less than a minute. We conclude that vibrational spectroscopy provides powerful means to detect changes in spores but it might be problematic to identify if spores are live or dead after a decontamination procedure.
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| 11. |
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| 12. |
- Mortezaei, Narges, et al.
(författare)
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Structural and biophysical comparison of UPEC and ETEC adhesion fimbriae
- 2015
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Ingår i: Biophysical Journal. - : Cell Press. - 0006-3495 .- 1542-0086. ; 108:2, suppl 1, s. 527A-527A
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Tidskriftsartikel (refereegranskat)abstract
- Adhesion fimbriae (pili) of uropathogenic and enterotoxigenic Escherichia coli (UPEC and ETEC, respectively) facilitate adherence of the bacteria to target cells. Fimbriae are absolutely necessary for colonization and biofilm formation in the initiation of disease. The types of fimbriae expressed on the bacterial surface vary with the preferred environmental niche of the bacterial strain. For example, UPEC that express P-pili are most frequently associated pyelonephritis, an infection in the upper urinary tract, whereas bacteria that express type 1 fimbriae commonly cause cystitis through infection of the lower urinary tract. In contrast, ETEC expressing CFA/I and CS2 pili are associated with diarrheal diseases, initiating disease in the small intestines.Although expressed in different enviroments, these fimbriae share basic structural and biomechanical features. Structurally, they are all long (1-4 μm), thin (7-8 nm diameter) helix-like filaments that extend from the bacterial surface. Biomechanically, they share the ability to be extended into a thinner filament (2-3 nm diameter) by unwinding of the helical filament under a constant force. However, the force required to unwind is specific to each fimbrial type. In addition, the dependence of the force required to unwind a fimbria on the velocity of this unwinding, (that is, the kinetics of unwinding), is also type-specific and highly variable. These biomechanical parameters are dissimilar for UPEC and ETEC expressed fimbriae, separating them into two distinct groups. Using force spectroscopy data, helical reconstructions from electron microscopy data, and computational simulations, we show in this work how these pronounced biomechanical differences may be beneficial for bacterial survival in a given environment.
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| 13. |
- Nilsson, Daniel P.G., et al.
(författare)
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Physico-chemical characterization of single bacteria and spores using optical tweezers
- 2023
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Ingår i: Research in Microbiology. - : Elsevier. - 0923-2508 .- 1769-7123. ; 174:6
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Tidskriftsartikel (refereegranskat)abstract
- Spore-forming pathogenic bacteria are adapted for adhering to surfaces, and their endospores can tolerate strong chemicals making decontamination difficult. Understanding the physico-chemical properties of bacteria and spores is therefore essential in developing antiadhesive surfaces and disinfection techniques. However, measuring physico-chemical properties in bulk does not show the heterogeneity between cells. Characterizing bacteria on a single-cell level can thereby provide mechanistic clues usually hidden in bulk measurements. This paper shows how optical tweezers can be applied to characterize single bacteria and spores, and how physico-chemical properties related to adhesion, fluid dynamics, biochemistry, and metabolic activity can be assessed.
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| 14. |
- Nilsson, Daniel, et al.
(författare)
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Patient-specific brain arteries molded as a flexible phantom model using 3D printed water-soluble resin
- 2022
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Visualizing medical images from patients as physical 3D models (phantom models) have many roles in the medical field, from education to preclinical preparation and clinical research. However, current phantom models are generally generic, expensive, and time-consuming to fabricate. Thus, there is a need for a cost- and time-efficient pipeline from medical imaging to patient-specific phantom models. In this work, we present a method for creating complex 3D sacrificial molds using an off-the-shelf water-soluble resin and a low-cost desktop 3D printer. This enables us to recreate parts of the cerebral arterial tree as a full-scale phantom model (10×6×410×6×4 cm) in transparent silicone rubber (polydimethylsiloxane, PDMS) from computed tomography angiography images (CTA). We analyzed the model with magnetic resonance imaging (MRI) and compared it with the patient data. The results show good agreement and smooth surfaces for the arteries. We also evaluate our method by looking at its capability to reproduce 1 mm channels and sharp corners. We found that round shapes are well reproduced, whereas sharp features show some divergence. Our method can fabricate a patient-specific phantom model with less than 2 h of total labor time and at a low fabrication cost.
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| 15. |
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| 16. |
- Norqvist, Patrik, et al.
(författare)
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Hollywoodfysik : undervisande underhållning
- 2006
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Ingår i: Fysikaktuellt. - Stockholm : Svenska fysikersamfundet. - 0283-9148. ; :4, s. 12-13
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 17. |
- Rodriguez, Alvaro, et al.
(författare)
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Refining particle positions using circular symmetry
- 2017
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Ingår i: PLOS ONE. - : Public Library of Science. - 1932-6203. ; 12:4
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Tidskriftsartikel (refereegranskat)abstract
- Particle and object tracking is gaining attention in industrial applications and is commonly applied in: colloidal, biophysical, ecological, and micro-fluidic research. Reliable tracking information is heavily dependent on the system under study and algorithms that correctly determine particle position between images. However, in a real environmental context with the presence of noise including particular or dissolved matter in water, and low and fluctuating light conditions, many algorithms fail to obtain reliable information. We propose a new algorithm, the Circular Symmetry algorithm (C-Sym), for detecting the position of a circular particle with high accuracy and precision in noisy conditions. The algorithm takes advantage of the spatial symmetry of the particle allowing for subpixel accuracy. We compare the proposed algorithm with four different methods using both synthetic and experimental datasets. The results show that C-Sym is the most accurate and precise algorithm when tracking micro-particles in all tested conditions and it has the potential for use in applications including tracking biota in their environment.
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| 18. |
- Shukla, Padma, et al.
(författare)
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Excitation of zonal flows by electron convective cells in a nonuniform dusty magnetoplasma
- 2001
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Ingår i: Physics Letters A. - 0375-9601 .- 1873-2429. ; 283:5-6, s. 371-375
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Tidskriftsartikel (refereegranskat)abstract
- It is shown that the ponderomotive force of electron convective cells can generate zonal flows (or dust convective cells) in a nonuniform magnetoplasma. For this purpose, two fluid equations are used to derive a pair of coupled equations which govern the nonlinear coupling between electron and dust convective cells. A dispersion relation for the parametric interactions is deduced from the mode coupling equations. Explicit expressions for the growth rates of electron convective cell driven zonal flows are then obtained. The relevance of our investigation to laboratory and space plasmas is pointed out.
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| 19. |
- Stangner, Tim, et al.
(författare)
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Cooke-Triplet-Tweezers : More compact, robust and efficient optical tweezers
- 2018
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Ingår i: Optics Letters. - 0146-9592 .- 1539-4794. ; 43:9, s. 1990-1993
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Tidskriftsartikel (refereegranskat)abstract
- We present a versatile three-lens optical design to improve the overall compactness, efficiency, and robustness for optical tweezers based applications. The design, inspired by the Cooke–Triplet configuration, allows for continuous beam magnifications of 2–10× , and axial as well as lateral focal shifts can be realized without switching lenses or introducing optical aberrations. We quantify the beam quality and trapping stiffness and compare the Cooke–Triplet design with the commonly used double Kepler design through simulations and direct experiments. Optical trapping of 1 and 2 μm beads shows that the Cooke–Triplet possesses an equally strong optical trap stiffness compared to the double Kepler lens design but reduces its lens system length by a factor of 2.6. Finally, we demonstrate how a Twyman–Green interferometer integrated in the Cooke–Triplet optical tweezers setup provides a fast and simple method to characterize the wavefront aberrations in the lens system and how it can help in aligning the optical components perfectly.
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| 20. |
- Stangner, Tim, et al.
(författare)
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Step-by-step guide to reduce spatial coherence of laser light using a rotating ground glass diffuser
- 2017
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Ingår i: Applied Optics. - : Optical Society of America. - 1559-128X .- 2155-3165. ; 56:19, s. 5427-5435
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Tidskriftsartikel (refereegranskat)abstract
- Wide field-of-view imaging of fast processes in a microscope requires high light intensities motivating the use of lasers as light sources. However, due to their long spatial coherence length, lasers are inappropriate for such applications, as they produce coherent noise and parasitic reflections, such as speckle, degrading image quality. Therefore, we provide a step-by-step guide for constructing a speckle-free and high-contrast laser illumination setup using a rotating ground glass diffuser driven by a stepper motor. The setup is easy to build, cheap, and allows a significant light throughput of 48%, which is 40% higher in comparison to a single lens collector commonly used in reported setups. This is achieved by using only one objective to collect the scattered light from the ground glass diffuser. We validate our setup in terms of image quality, speckle contrast, motor-induced vibrations, and light throughput. To highlight the latter, we record Brownian motion of micro-particles using a 100x oil immersion objective and a high-speed camera operating at 2000 Hz with a laser output power of only 22 mW. Moreover, by reducing the objective magnification to 50x, sampling rates up to 10,000 Hz are realized. To help readers with basic or advanced optics knowledge realize this setup, we provide a full component list, 3D-printing CAD files, setup protocol, and the code for running the stepper motor.
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| 21. |
- Wiklund, Krister, et al.
(författare)
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A drag force interpolation model for capsule-shaped cells in fluid flows near a surface
- 2018
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Ingår i: Microbiology. - : Microbiology Society. - 1350-0872 .- 1465-2080. ; 164:4, s. 483-494
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Tidskriftsartikel (refereegranskat)abstract
- We report an interpolation model to calculate the hydrodynamic force on tethered capsule-shaped cells in micro-fluidic flows near a surface. Our model is based on numerical solutions of the full Navier–Stokes equations for capsule-shaped objects considering their geometry, aspect ratio and orientation with respect to fluid flow. The model reproduced the results from computational fluid dynamic simulations, with an average error of <0.15 % for objects with an aspect ratio up to 5, and the model exactly reproduced the Goldman approximation of spherical objects close to a surface. We estimated the hydrodynamic force imposed on tethered Escherichia coli cells using the interpolation model and approximate models found in the literature, for example, one that assumes that E. coli is ellipsoid shaped. We fitted the 2D-projected area of a capsule and ellipsoid to segmented E. coli cells. We found that even though an ellipsoidal shape is a reasonable approximation of the cell shape, the capsule gives 4.4 % better agreement, a small difference that corresponds to 15 % difference in hydrodynamic force. In addition, we showed that the new interpolation model provides a significantly better agreement compared to estimates from commonly used models and that it can be used as a fast and accurate substitute for complex and computationally heavy fluid dynamic simulations. This is useful when performing bacterial adhesion experiments in parallel-plate flow channels. We include a MATLAB script that can track cells in a video time-series and estimate the hydrodynamic force using our interpolation formula.
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| 22. |
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| 23. |
- Wiklund, Krister, et al.
(författare)
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Hermitian structure for linear internal waves in sheared flow
- 2001
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Ingår i: Physics Letters A. - 0375-9601 .- 1873-2429. ; 279:1-2, s. 67-69
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Tidskriftsartikel (refereegranskat)abstract
- Motivated by the problem of linear mode conversion between ducted internal gravity waves in a sheared flow, we construct a variational principle based on a Hermitian evolution operator, obtained from Larsson's Hamiltonian formalism.
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| 24. |
- Wiklund, Krister, et al.
(författare)
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Mode coupling and stability of modified convective cells in a nonuniform dusty magnetoplasma
- 2001
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Ingår i: Physics Letters A. - 0375-9601 .- 1873-2429. ; 279:3-4, s. 239-242
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Tidskriftsartikel (refereegranskat)abstract
- Within the framework of a Hamiltonian approach, we study mode coupling and stability of nonlinearly interacting modified convective cells in a nonuniform dusty magnetoplasma. Expressions for the coupling coefficients and a stability criterion for the stationary solutions are presented. This is a necessary prerequisite for understanding the nonlinear dynamics of convective cells in a dusty magnetoplasma with a strongly nonuniform background.
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| 25. |
- Wiklund, Krister
(författare)
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Wave interactions by Hamiltonian methods
- 2002
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is devoted to the description of fluids and gases from a Hamiltonian point of view. The method we apply is a development of the theory invented by Hamilton (1805-1865). The original formulation is restricted to a certain family of dynamical variables; the canonical variables. In fluid dynamics, however, an extension to a noncanonical formulation is necessary, at least if we want to benefit from the Hamiltonian machinery and simultaneously want to use variables with a simple physical interpretation.The noncanonical Hamiltonian structure of the fluid equations can be utilized for several applications. We apply it to nonlinear wave interaction problems for fluid descriptions like the vorticity equation, the shallow-water equation, a family of Hasegawa-Mima-like equations and the equations describing dusty magnetoplasmas. The Hamiltonian structure is used to simplify the calculation of the strength of the coupling between the waves.Another important application concerns the question of finding fluid states that are stable against small perturbations. The Hamiltonian formulation is in this case an effective tool, and the derivation of explicit stability criteria is simplified.The first chapter of this thesis gives a brief and informal introduction to fluid dynamics. In chapter two we present, in a more formal way, some important fluid equations. Chapter three contains a discussion of variational principles and offers a first glance of Hamiltonian theory. The generalisation of this theory is the main subject of the first sections of chapter four, and we finish this chapter by presenting some applications of the general Hamiltonian theory. These applications which involve several different fluid systems are presented in the six papers included in this thesis. In the main, they concern the explicit calculation of symmetrical coupling coefficients and the derivation of sufficient conditions for stability. Some of the results, however, deals with the influence of boundaries in the vorticity equation and the construction of variational principles for the linearised system.
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| 26. |
- Wiklund, Krister
(författare)
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Wave interactions in a shallow-water model
- 1998
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Ingår i: Nonlinear processes in geophysics. - : Copernicus GmbH. - 1023-5809 .- 1607-7946. ; 5:3, s. 137-144
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Tidskriftsartikel (refereegranskat)abstract
- By using a Hamiltonian method, non-linear three-wave interaction in a class of systems related to the shallow water model is considered and a general coupling coefficient is presented. In the special case where two inertial waves and one Rossby wave interact resonantly, it is found that even a very small shear of the background velocity can be important in the interaction process. The stability of the system is considered by using a pseudoenergy method. Some implications for the dynamics of atmospheric flows are pointed out.
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| 27. |
- Wittmann, Philipp, 1992-
(författare)
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The Jovian Plasma Dynamics and Composition Analyzer (JDC) for ESA's JUICE Mission
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This dissertation covers the development and calibration of the Jovian plasma Dynamics and Composition analyzer (JDC). JDC is together with five other sensors a part of the Particle Environment Package (PEP), one of the payloads of the European Space Agency's JUpiter ICy moons Explorer (JUICE) mission. The JUICE mission is designed to broaden our understanding of the Jovian system including Jupiter, the four Galilean moons (Io, Europa, Ganymede and Callisto) and Jupiter's vast magnetosphere. JUICE is planned to launch in 2023.The PEP payload will study the plasma environment around Jupiter and its moons in great detail. As one of the sensors of PEP, JDC will measure the energy distribution of positive and negative ions as well as electrons in an energy range from a few eV/q up to 35keV/q. The field of view covered by JDC spans over a full hemisphere. JDC also determines the mass of particles using the time-of-flight principle. Alternatively, there is the possibility to determine the distribution of particle arrival times to study their distribution in the time domain.In this thesis, ion-optical, mechanical, electrical, thermal, radiation shielding and instrument operation related design solutions are presented and discussed. Special attention was paid to the performance of the channel electron multipliers used as time-of-flight start detectors. To verify their performance throughout the whole mission, a full lifetime test for these detectors was successfully performed. As a result of this test a qualitative performance model for channel electron multipliers was developed. Another experiment included in this work is the determination of the residual gas pressure evolution inside of JDC. A sufficiently low residual gas pressure is required for safe operation of JDC's high voltage systems. Finally, the performance of the JDC linear electric field reflectron was verified using a dedicated prototype.The last part of this work describes the methods used for instrument calibration and first results of the calibration of the flight spare model of JDC, the unit that will fly to Jupiter, are presented.
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| 28. |
- Zakrisson, Johan, et al.
(författare)
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Detecting Bacterial Surface Organelles on Single Cells using Optical Tweezers
- 2016
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 32:18, s. 4521-4529
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial cells display a diverse array of surface organelles that are important for a range of processes such as: intercellular communication, motility and adhesion leading to biofilm formation, infections and bacterial spread. More specifically, attachment to host cells by Gram-negative bacteria are mediated by adhesion pili, which are nm wide and µm long fibrous organelles. Since these pili are significantly thinner than the wavelength of visible light, they cannot be detected using standard light microscopy techniques. At present, there is no fast and simple method available to investigate if a single cell expresses pili while keeping the cell alive for further studies. In this study, we present a method to determine the presence of pili on a single bacterium. The protocol involves imaging the bacterium to measure its size, followed by predicting the fluid drag based on its size using an analytical model, and thereafter oscillating the sample while a single bacterium is trapped by an optical tweezer to measure its effective fluid drag. Comparison between the predicted and the measured fluid drag thereby indicate the presence of pili. Herein, we verify the method using polymer coated silica microspheres and Escherichia coli bacteria expressing adhesion pili. Our protocol, can in real time and within seconds assist single cell studies by distinguishing between piliated and non-piliated bacteria.
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| 29. |
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| 30. |
- Zakrisson, Johan, et al.
(författare)
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Helix-like bio-polymers can act as effective dampers for bacteria in flows
- 2012
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Ingår i: European Biophysics Journal. - Springer : Springer Science and Business Media LLC. - 0175-7571 .- 1432-1017. ; 41:6, s. 551-560
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Tidskriftsartikel (refereegranskat)abstract
- Biopolymers are vital structures for many liv- ing organisms; for a variety of bacteria, adhesion polymers play a crucial role for the initiation of colonization. Some bacteria express, on their surface, attachment organelles (pili) that comprise subunits formed into stiff helix-like structures that possess unique biomechanical properties. These helix-like structures possess a high degree of flexi- bility that gives the biopolymers a unique extendibility. This has been considered beneficial for piliated bacteria adhering to host surfaces in the presence of a fluid flow. We show in this work that helix-like pili have the ability to act as efficient dampers of force that can, for a limited time, lower the load on the force-mediating adhesin-receptor bond on the tip of an individual pilus. The model presented is applied to bacteria adhering with a single pilus of either of the two most common types expressed by uropathogenic Escherichia coli, P or type 1 pili, subjected to realistic flows. The results indicate that for moderate flows (~25 mm/s) the force experienced by the adhesin-receptor interaction at the tip of the pilus can be reduced by a factor of ~6 and ~4, respectively. The uncoiling ability pro- vides a bacterium with a ‘‘go with the flow’’ possibility that acts as a damping. It is surmised that this can be an important factor for the initial part of the adhesion process, in particular in turbulent flows, and thereby be of use for bacteria in their striving to survive a natural defense such as fluid rinsing actions.
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| 31. |
- Zakrisson, Johan, et al.
(författare)
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Rigid multibody simulation of a helix-like structure : the dynamics of bacterial adhesion pili
- 2015
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Ingår i: European Biophysics Journal. - : Springer Science and Business Media LLC. - 0175-7571 .- 1432-1017. ; 44:5, s. 291-300
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Tidskriftsartikel (refereegranskat)abstract
- We present a coarse-grained rigid multibody model of a subunit assembled helix-like polymer, e.g., adhesion pili expressed by bacteria, that is capable of describing the polymer's force-extension response. With building blocks representing individual subunits, the model appropriately describes the complex behavior of pili expressed by the gram-negative uropathogenic Escherichia coli bacteria under the action of an external force. Numerical simulations show that the dynamics of the model, which include the effects of both unwinding and rewinding, are in good quantitative agreement with the characteristic force-extension response as observed experimentally for type 1 and P pili. By tuning the model, it is also possible to reproduce the force-extension response in the presence of anti-shaft antibodies, which dramatically changes the mechanical properties. Thus, the model and results in this work give enhanced understanding of how a pilus unwinds under the action of external forces and provide a new perspective of the complex bacterial adhesion processes.
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| 32. |
- Zakrisson, Johan, et al.
(författare)
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Tethered cells in fluid flows : beyond the Stokes’ drag force approach
- 2015
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Ingår i: Physical Biology. - : IOP Publishing. - 1478-3967 .- 1478-3975. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Simulations of tethered cells in viscous sub-layers are frequently performed using the Stokes' drag force, but without taking into account contributions from surface corrections, lift forces, buoyancy, the Basset force, the cells' finite inertia, or added mass. In this work, we investigate to what extent such contributions, under a variety of hydrodynamic conditions, influence the force at the anchor point of a tethered cell and the survival probability of a bacterium that is attached to a host by either a slip or a catch bond via a tether with a few different biomechanical properties. We show that a consequence of not including some of these contributions is that the force to which a bond is exposed can be significantly underestimated; in general by similar to 32-46%, where the influence of the surface corrections dominate ( the parallel and normal correction coefficients contribute similar to 5-8 or similar to 23-26%, respectively). The Basset force is a major contributor, up to 20%, for larger cells and shear rates. The lift force and inertia contribute when cells with radii >3 mu m have shear rates>2000 s(-1). Buoyancy contributes significantly for cells with radii > 3 mu m for shear rates<10 s(-1). Since the lifetime of a bond depends strongly on the force, both the level of approximation and the biomechanical model of the tether significantly affect the survival probability of tethered bacteria. For a cell attached by a FimH-mannose bond and an extendable tether with a shear rate of 3000 s(-1), neglecting the surface correction coefficients or the Basset force can imply that the survival probability is overestimated by more than an order of magnitude. This work thus shows that in order to quantitatively assess bacterial attachment forces and survival probabilities, both the fluid forces and the tether properties need to be modeled accurately.
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| 33. |
- Zakrisson, Johan, et al.
(författare)
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The shaft of the type 1 fimbriae regulates an externalforce to match the FimH catch bond
- 2013
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 104:10, s. 2137-2148
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Tidskriftsartikel (refereegranskat)abstract
- Type 1 fimbriae mediate adhesion of uropathogenic Escherichia coli to host cells. It has been hypothesized that due to their ability to uncoil under exposure to force, fimbriae can reduce fluid shear stress on the adhesin-receptor interaction by which the bacterium adheres to the surface. In this work, we develop a model that describes how the force on the adhesin-receptor interaction of a type 1 fimbria varies as a bacterium is affected by a time-dependent fluid flow mimicking in vivo conditions. The model combines in vivo hydrodynamic conditions with previously assessed biomechanical properties of the fimbriae. Numerical methods are used to solve for the motion and adhesion force under the presence of time-dependent fluid profiles. It is found that a bacterium tethered with a type 1 pilus will experience significantly reduced shear stress for moderate to high flow velocities and that the maximum stress the adhesin will experience is limited to ∼120 pN, which is sufficient to activate the conformational change of the FimH adhesin into its stronger state but also lower than the force required for breaking it under rapid loading. Our model thus supports the assumption that the type 1 fimbria shaft and the FimH adhesin-receptor interaction are optimized to each other, and that they give piliated bacteria significant advantages in rapidly changing fluidic environments.
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| 34. |
- Zhang, Hanqing, 1988-
(författare)
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Digital holography and image processing methods for applications in biophysics
- 2018
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Understanding dynamic mechanisms, morphology and behavior of bacteria are important to develop new therapeutics to cure diseases. For example, bacterial adhesion mechanisms are prerequisites for initiation of infections and for several bacterial strains this adhesion process is mediated by adhesive surface organelles, also known as fimbriae. Escherichia coli (E. coli) is a bacterium expressing fimbriae of which pathogenic strains can cause severe diseases in fluidic environments such as the urinary tract and intestine. To better understand how E. coli cells attach and remain attached to surfaces when exposed to a fluid flow using their fimbriae, experiments using microfluidic channels are important; and to assess quantitative information of the adhesion process and cellular information of morphology, location and orientation, the imaging capability of the experimental technique is vital.In-line digital holographic microscopy (DHM) is a powerful imaging technique that can be realized around a conventional light microscope. It is a non-invasive technique without the need of staining or sectioning of the sample to be observed in vitro. DHM provides holograms containing three-dimensional (3D) intensity and phase information of cells under study with high temporal and spatial resolution. By applying image processing algorithms to the holograms, quantitative measurements can provide information of position, shape, orientation, optical thickness of the cell, as well as dynamic cell properties such as speed, growing rate, etc.In this thesis, we aim to improve the DHM technique and develop image processing methods to track and assess cellular properties in microfluidic channels to shed light on bacterial adhesion and cell morphology. To achieve this, we implemented a DHM technique and developed image processing algorithms to provide for a robust and quantitative analysis of holograms. We improved the cell detection accuracy and efficiency in DHM holograms by developing an algorithm for detection of cell diffraction patterns. To improve the 3D detection accuracy using in-line digital holography, we developed a novel iterative algorithm that use multiple-wavelengths. We verified our algorithms using synthetic, colloidal and cell data and applied the algorithms for detecting, tracking and analysis. We demonstrated the performance when tracking bacteria with sub-micrometer accuracy and kHz temporal resolution, as well as how DHM can be used to profile a microfluidic flow using a large number of colloidal particles. We also demonstrated how the results of cell shape analysis based on image segmentation can be used to estimate the hydrodynamic force on tethered capsule-shaped cells in micro-fluidic flows near a surface.
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| 35. |
- Zhang, Hanqing, et al.
(författare)
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DSeg : a dynamic image segmentation program to extract backbone patterns for filamentous bacteria and hyphae structures
- 2019
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Ingår i: Microscopy and Microanalysis. - : Cambridge University Press. - 1431-9276 .- 1435-8115. ; 25:3, s. 711-719
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Tidskriftsartikel (refereegranskat)abstract
- Analysis of numerous filamentous structures in an image is often limited by the ability of algorithms to accurately segment complex structures or structures within a dense population. It is even more problematic if these structures continuously grow when recording a time-series of images. To overcome these issues we present DSeg; an image analysis program designed to process time-series image data, as well as single images, to segment filamentous structures. The program includes a robust binary level-set algorithm modified to use size constraints, edge intensity, and past information. We verify our algorithms using synthetic data, differential interference contrast images of filamentous prokaryotes, and transmission electron microscopy images of bacterial adhesion fimbriae. DSeg includes automatic segmentation, tools for analysis, and drift correction, and outputs statistical data such as persistence length, growth rate, and growth direction. The program is available at Sourceforge.
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| 36. |
- Zhang, Hanqing, et al.
(författare)
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Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolvedby iterative reconstruction routines. However, recovering the phase properties of an object in a hologramneeds an object plane to be chosen correctly for reconstruction. In this work, we present a novelmulti-wavelength Gerchberg-Saxton algorithm to determine the object plane using single-shot hologramsrecorded with multiple wavelengths in an in-line holographic microscope. For micro-sized objects, weverify the object positioning capabilities of the method for various shapes and derive the phase informationusing synthetic and experimental data. Experimentally, we built a compact digital in-line holographicmicroscopy setup around a standard optical microscope with a regular RGB-CCD camera andacquire holograms of micro-spheres, E. coli and red blood cells, that are illuminated using three lasersoperating at 491nm, 532nm and 633nm, respectively. We demonstrate that our method provides accurateobject plane detection and phase retrieval under noisy conditions, e.g., using low-contrast hologramswithout background normalization. This method allows for automatic positioning and phase retrievalsuitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.
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| 37. |
- Zhang, Hanqing, et al.
(författare)
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Object plane detection and phase retrieval from single-shot holograms using multi-wavelength in-line holography
- 2018
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Ingår i: Applied Optics. - : Optical Society of America. - 1559-128X .- 2155-3165. ; 57:33, s. 9855-9862
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Tidskriftsartikel (refereegranskat)abstract
- Phase retrieval and the twin-image problem in digital in-line holographic microscopy can be resolved by iterative reconstruction routines. However, recovering the phase properties of an object in a hologram requires an object plane to be chosen correctly for reconstruction. In this work, we present a novel multi-wavelength iterative algorithm to determine the object plane using single-shot holograms recorded at multiple wavelengths in an in-line holographic microscope. Using micro-sized objects, we verify the object positioning capabilities of the method for various shapes and derive the phase information using synthetic and experimental data. Experimentally, we built a compact digital in-line holographic microscopy setup around a standard optical microscope with a regular RGB-CCD camera and acquired holograms of micro-spheres, E. coli, and red blood cells, which are illuminated using three lasers operating at 491 nm, 532 nm, and 633 nm, respectively. We demonstrate that our method provides accurate object plane detection and phase retrieval under noisy conditions, e.g., using low-contrast holograms with an inhomogeneous background. This method allows for automatic positioning and phase retrieval suitable for holographic particle velocimetry, and object tracking in biophysical or colloidal research.
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| 38. |
- Zhang, Hanqing, et al.
(författare)
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UmUTracker : a versatile MATLAB program for automated particle tracking of 2D light microscopy or 3D digital holography data
- 2017
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Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 219, s. 390-399
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Tidskriftsartikel (refereegranskat)abstract
- We present a versatile and fast MATLAB program (UmUTracker) that automatically detects and tracks particles by analyzing video sequences acquired by either light microscopy or digital in-line holographic microscopy. Our program detects the 2D lateral positions of particles with an algorithm based on the isosceles triangle transform, and reconstructs their 3D axial positions by a fast implementation of the Rayleigh-Sommerfeld model using a radial intensity profile. To validate the accuracy and performance of our program, we first track the 2D position of polystyrene particles using bright field and digital holographic microscopy. Second, we determine the 3D particle position by analyzing synthetic and experimentally acquired holograms. Finally, to highlight the full program features, we profile the microfluidic flow in a 100 gm high flow chamber. This result agrees with computational fluid dynamic simulations. On a regular desktop computer UmUTracker can detect, analyze, and track multiple particles at 5 frames per second for a template size of 201 x 201 in a 1024 x 1024 image. To enhance usability and to make it easy to implement new functions we used object-oriented programming. UmUTracker is suitable for studies related to: particle dynamics, cell localization, colloids and microfluidic flow measurement.Program summaryProgram title: UmUTracker Program Files doi: http://dx.doi.org/10.17632/fkprs4s6xp.1Licensing provisions: Creative Commons by 4.0 (CC by 4.0)Programming language: MATLAB Nature of problem: 3D multi-particle tracking is a common technique in physics, chemistry and biology. However, in terms of accuracy, reliable particle tracking is a challenging task since results depend on sample illumination, particle overlap, motion blur and noise from recording sensors. Additionally, the computational performance is also an issue if, for example, a computationally expensive process is executed, such as axial particle position reconstruction from digital holographic microscopy data. Versatile robust tracking programs handling these concerns and providing a powerful post-processing option are significantly limited.Solution method: UmUTracker is a multi-functional tool to extract particle positions from long video sequences acquired with either light microscopy or digital holographic microscopy. The program provides an easy-to-use graphical user interface (GUI) for both tracking and post-processing that does not require any programming skills to analyze data from particle tracking experiments. UmUTracker first conduct automatic 2D particle detection even under noisy conditions using a novel circle detector based on the isosceles triangle sampling technique with a multi-scale strategy. To reduce the computational load for 3D tracking, it uses an efficient implementation of the Rayleigh-Sommerfeld light propagation model. To analyze and visualize the data, an efficient data analysis step, which can for example show 4D flow visualization using 3D trajectories, is included. Additionally, UmUTracker is easy to modify with user customized modules due to the object-oriented programming style.Additional comments: Program obtainable from https://sourceforge.net/projects/umutracker/
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