| 1. |
- Midtvedt, Benjamin, et al.
(författare)
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Single-shot self-supervised object detection in microscopy
- 2022
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
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| 2. |
- Midtvedt, Daniel, 1988, et al.
(författare)
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Direct measurement of nitric oxide (NO) in the gastrointestinal tract of cod (Gadus morhua)
- 2009
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Ingår i: Microbial Ecology in Health and Disease. - : Informa UK Limited. - 0891-060X .- 1651-2235. ; 21:3-4, s. 175-177
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Tidskriftsartikel (refereegranskat)abstract
- Objective: In mammals, the biological messenger nitric oxide (NO) is generated throughout the gastrointestinal (GI) tract from the reduction of dietary nitrate and nitrite. The aim of the present study was to investigate the amount of GI NO in Atlantic cod (Gadus morhua) in relation to intake of food. Methods: A total of 28 cod were divided into 3 groups, fed at different times before the experiment (1 week, 1 day, and 3 h, respectively). Results: In the stomach, the measured NO concentrations were consistently higher in the group fed 3 h before the measurement, implying that the NO3-NO2-NO pathway is present in the stomach of cod. We also measured the NO concentration in the large intestine. Again, the values were higher in cod fed 3 h before the experiment. Conclusion: We conclude that NO is formed in the GI tract of cod, likely via the reduction of dietary nitrate and nitrite. The physiological importance of this NO production remains to be determined.
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| 3. |
- Parveen, Nagma, 1988, et al.
(författare)
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Membrane Deformation Induces Clustering of Norovirus Bound to Glycosphingolipids in a Supported Cell-Membrane Mimic
- 2018
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Ingår i: Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 9:9, s. 2278-2284
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Tidskriftsartikel (refereegranskat)abstract
- Quartz crystal microbalance with dissipation monitoring and total internal reflection fluorescence microscopy have been used to investigate binding of norovirus-like particles (noroVLPs) to a supported (phospho)lipid bilayer (SLB) containing a few percent of H or B type 1 glycosphingolipid (GSL) receptors. Although neither of these GSLs spontaneously form domains, noroVLPs were observed to form micron-sized clusters containing typically up to about 30 VLP copies, especially for B type 1, which is a higher-affinity receptor. This novel finding is explained by proposing a model implying that VLP-induced membrane deformation promotes VLP clustering, a hypothesis that was further supported by observing that functionalized gold nanoparticles were able to locally induce SLB deformation. Because similar effects are likely possible also at cellular membranes, our findings are interesting beyond a pure biophysicochemical perspective as they shed new light on what may happen during receptor-mediated uptake of viruses as well as nanocarriers in drug delivery. © Copyright 2018 American Chemical Society.
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| 4. |
- Abuhattum, Shada, et al.
(författare)
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Intracellular Mass Density Increase Is Accompanying but Not Sufficient for Stiffening and Growth Arrest of Yeast Cells
- 2018
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Ingår i: Frontiers in Physics. - : Frontiers Media SA. - 2296-424X. ; 6:NOV
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Tidskriftsartikel (refereegranskat)abstract
- Many organisms, including yeast cells, bacteria, nematodes, and tardigrades, endure harsh environmental conditions, such as nutrient scarcity, or lack of water and energy for a remarkably long time. The rescue programs that these organisms launch upon encountering these adverse conditions include reprogramming their metabolism in order to enter a quiescent or dormant state in a controlled fashion. Reprogramming coincides with changes in the macromolecular architecture and changes in the physical and mechanical properties of the cells. However, the cellular mechanisms underlying the physical-mechanical changes remain enigmatic. Here, we induce metabolic arrest of yeast cells by lowering their intracellular pH. We then determine the differences in the intracellular mass density and stiffness of active and metabolically arrested cells using optical diffraction tomography (ODT) and atomic force microscopy (AFM). We show that an increased intracellular mass density is associated with an increase in stiffness when the growth of yeast is arrested. However, increasing the intracellular mass density alone is not sufficient for maintenance of the growth-arrested state in yeast cells. Our data suggest that the cytoplasm of metabolically arrested yeast displays characteristics of a solid. Our findings constitute a bridge between the mechanical behavior of the cytoplasm and the physical and chemical mechanisms of metabolically arrested cells with the ultimate aim of understanding dormant organisms.
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| 5. |
- Croy, Alexander, 1981, et al.
(författare)
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Nonlinear damping in graphene resonators
- 2012
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Ingår i: Physical Review B - Condensed Matter and Materials Physics. - 2469-9950 .- 2469-9969. ; 86:23, s. Article Number: 235435-
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Tidskriftsartikel (refereegranskat)abstract
- Based on a continuum mechanical model for single-layer graphene, we propose and analyze a microscopic mechanism for dissipation in nanoelectromechanical graphene resonators. We find that coupling between flexural modes and in-plane phonons leads to linear and nonlinear damping of out-of-plane vibrations. By tuning external parameters such as bias and ac voltages, one can cross over from a linear-to a nonlinear-damping dominated regime. We discuss the behavior of the effective quality factor in this context. DOI: 10.1103/PhysRevB.86.235435
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| 6. |
- Eriksson, Martin, 1989, et al.
(författare)
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Frequency tuning, nonlinearities and mode coupling in circular mechanical graphene resonators
- 2013
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Ingår i: Nanotechnology. - : IOP Publishing. - 1361-6528 .- 0957-4484. ; 24:39, s. srt. no. 395702-
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Tidskriftsartikel (refereegranskat)abstract
- We study circular nanomechanical graphene resonators by means of continuum elasticity theory, treating them as membranes. We derive dynamic equations for the flexural mode amplitudes. Due to the geometrical nonlinearity the mode dynamics can be modeled by coupled Duffing equations. By solving the Airy stress problem we obtain analytic expressions for the eigenfrequencies and nonlinear coefficients as functions of the radius, suspension height, initial tension, back-gate voltage and elastic constants, which we compare with finite element simulations. Using perturbation theory, we show that it is necessary to include the effects of the non-uniform stress distribution for finite deflections. This correctly reproduces the spectrum and frequency tuning of the resonator, including frequency crossings.
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| 7. |
- Lindahl, Niklas, 1981, et al.
(författare)
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Determination of the Bending Rigidity of Graphene via Electrostatic Actuation of Buckled Membranes
- 2012
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Ingår i: Nano Letters. - : American Chemical Society (ACS). - 1530-6984 .- 1530-6992. ; 12:7, s. 3526-3531
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Tidskriftsartikel (refereegranskat)abstract
- Classical continuum mechanics is used extensively to predict the properties of nanoscale materials such as graphene. The bending rigidity, kappa, is an important parameter that is used, for example, to predict the performance of graphene nanoelectromechanical devices and also ripple formation. Despite its importance, there is a large spread in the theoretical predictions of kappa for few-layer graphene. We have used the snap-through behavior of convex buckled graphene membranes under the application of electrostatic pressure to determine experimentally values of kappa for double-layer graphene membranes. We demonstrate how to prepare convex-buckled suspended graphene ribbons and fully clamped suspended membranes and show how the determination of the curvature of the membranes and the critical snap-through voltage, using AFM, allows us to extract kappa. The bending rigidity of bilayer graphene membranes under ambient conditions was determined to be 35.5(-15.0)(+20.0) eV. Monolayers are shown to have significantly lower kappa than bilayers.
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| 8. |
- Midtvedt, Daniel, 1988
(författare)
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Elastic properties of suspended graphene
- 2012
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns describing the mechanical properties of the two dimensional material graphene by continuum elasticity theory. In particular, Nano ElectroMechanical Systems (NEMS) where part of the graphene sheet is made suspended, are considered.In the first paper, the motion of a suspended graphene sheet is used to enhance the operation of a carbon nanotube field effect transistor. Here, the suspended graphene is used as a top-gate, controlling the charge density on the carbon nanotube channel. It is shown that the motion of the graphene sheet increases the sensitivity of the charge density on the carbon nanotube to the applied gate voltage.A factor limiting the applicability of mechanical resonators in electronics is damping of the mechanical motion. In an ongoing project, a specific mode of dissipation, namely the coupling between the flexural motion of the graphene sheet to phonons in the graphene and the underlying substrate, is investigated on a theoretical basis. It is found that this mechanism gives rise to both linear and amplitude dependent (nonlinear) damping.In paper II, the rigidity of graphene toward bending is investigated in collaboration with an experimental group at Gothenburg University. Here, compressive strain was built up in the graphene membrane through thermal cycling. Upon making the membrane suspended, the strain was released, causing the graphene to buckle. This type of buckled structures display an instability at a certain critical pressure. This critical pressure was then related to the bending rigidity of graphene. The bending rigidity was measured both for bilayered and monolayered graphene, with the result $\kappa_{Bi}\approx 30^{+20}_{-15}$eV and $\kappa_{Mono}\approx 7^{+4}_{-3}$ eV.
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| 9. |
- Midtvedt, Daniel, 1988, et al.
(författare)
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Fermi-Pasta-Ulam Physics with Nanomechanical Graphene Resonators: Intrinsic Relaxation and Thermalization from Flexural Mode Coupling
- 2014
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 112:14
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Tidskriftsartikel (refereegranskat)abstract
- Thermalization in nonlinear systems is a central concept in statistical mechanics and has been extensively studied theoretically since the seminal work of Fermi, Pasta, and Ulam. Using molecular dynamics and continuum modeling of a ring-down setup, we show that thermalization due to nonlinear mode coupling intrinsically limits the quality factor of nanomechanical graphene drums and turns them into potential test beds for Fermi-Pasta-Ulam physics. We find the thermalization rate Gamma to be independent of radius and scaling as Gamma similar to T* /is an element of(2)(pre), where T* and is an element of(pre) are effective resonator temperature and prestrain.
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| 10. |
- Midtvedt, Daniel, 1988, et al.
(författare)
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Label-free spatio-temporal monitoring of cytosolic mass, osmolarity, and volume in living cells
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Microorganisms adapt their biophysical properties in response to changes in their local environment. However, quantifying these changes at the single-cell level has only recently become possible, largely relying on fluorescent labeling strategies. In this work, we utilize yeast (Saccharomyces cerevisiae) to demonstrate label-free quantification of changes in both intracellular osmolarity and macromolecular concentration in response to changes in the local environment. By combining a digital holographic microscope with a millifluidic chip, the temporal response of cellular water flux was successfully isolated from the rate of production of higher molecular weight compounds, in addition to identifying the produced compounds in terms of the product of their refractive index increment (dndc) and molar mass. The ability to identify, quantify and temporally resolve multiple biophysical processes in living cells at the single cell level offers a crucial complement to label-based strategies, suggesting broad applicability in studies of a wide-range of cellular processes.
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