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  • 1.
    Lindahl, Viveca
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Lidmar, Jack
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Sampling rare biomolecular events with adaptive pulling simulations2015In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S144-S144Article in journal (Other academic)
  • 2.
    Mårtensson, Gustaf
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Skote, Martin
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Malmqvist, Mats
    Falk, Mats
    Asp, Allan
    Svanvik, Nicke
    Johansson, Arne V.
    Rapid PCR amplification of DNA utilizing Coriolis effects2006In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 35, no 6, p. 453-458Article in journal (Refereed)
    Abstract [en]

    A novel polymerase chain reaction (PCR) method is presented that utilizes Coriolis and centrifugal effects, produced by rotation of the sample disc, in order to increase internal circulatory rates, and with them temperature homogenization and mixing speeds. A proof of concept has been presented by testing a rapid 45-cycle PCR DNA amplification protocol. During the repeated heating and cooling that constitutes a PCR process, the 100 mu L samples were rotated at a speed equivalent to an effective acceleration of gravity of 7,000 g. A cycle time of 20.5 s gave a total process time of 15 min to complete the 45 cycles. A theoretical and numerical analysis of the resulting flow, which describes the increased mixing and temperature homogenization, is presented. The device gives excellent reaction speed efficiency, which is beneficial for rapid PCR.

  • 3.
    Rigler, Rudolf
    et al.
    Karolinska Inst, Dept Med Biochem & Biophys, Stockholm, Sweden..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Fluorescence-based monitoring of electronic state and ion exchange kinetics with FCS and related techniques: from T-jump measurements to fluorescence fluctuations2018In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 47, no 4, p. 479-492Article in journal (Refereed)
    Abstract [en]

    In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later. FCS can be used for monitoring reaction kinetics, based on fluctuations at thermodynamic equilibrium, rather than on relaxation measurements following perturbations. In this review, we more specifically discuss FCS measurements on photodynamic, electronic state transitions in fluorophore molecules, and on proton exchange dynamics in solution and on biomembranes. In the latter case, FCS measurements have proven capable of casting new light on the mechanisms of proton exchange at biological membranes, of central importance to bioenergetics and signal transduction. Finally, we describe the transient-state (TRAST) spectroscopy/imaging technique, sharing features with both relaxation (T-jump) and equilibrium fluctuation (FCS) techniques. TRAST is broadly applicable for cellular and molecular studies, and we briefly outline how TRAST can provide unique information from fluorophore blinking kinetics, reflecting e.g., cellular metabolism, rare molecular encounters, and molecular stoichiometries.

  • 4.
    Saeedimasine, M.
    et al.
    Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden..
    Montanino, Annaclauida
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Kleiven, Svein
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Neuronic Engineering.
    Villa, A.
    Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden..
    Impact of lipid composition and ion channel on the mechanical behavior of axonal membranes: a molecular simulation study2019In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 48, p. S99-S99Article in journal (Other academic)
  • 5.
    Stilbs, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Automated CORE, RECORD, and GRECORD processing of multi-component PGSE NMR diffusometry data2013In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 42, no 1, p. 25-32Article in journal (Refereed)
    Abstract [en]

    Pulsed gradient spin-echo (PGSE) NMR techniques have found growing and widespread use for investigation of a variety of physicochemical phenomena in solution, because of their effect on molecular self-diffusion, and for primarily analytical purposes, for example separation of overlapping NMR bandshapes obtained from multi-component samples. A multi-component spectral separation approach previously introduced by the author (named CORE) is founded on the fact that each part of a molecule diffuses at the same rate, and thus PGSE NMR signals from each functional group will attenuate in a fully concerted fashion throughout a PGSE experiment. Numerical separation and analysis of component NMR spectra by CORE processing is therefore stabilized and steered by this prior knowledge constraint. However, even with two components and with similar self-diffusion rates, numerical instability and cross-talk between similar component self-diffusion may appear even with good experimental signal-to-noise ratio and only minor or no component spectral overlap. So-called RECORD processing was recently introduced to accompany the CORE method. In this more robust variant, spectra are divided into several sub-regions that are treated separately and combined in a later stage. The rationale for and advantages of the generic RECORD-based approach are further discussed and illustrated. A further hybrid CORE processing variant named GRECORD is suggested and briefly tested.

  • 6.
    Ullmann, R. T.
    et al.
    MPI Biophys, Theoret & Computat Biophys, Gottingen, Germany..
    Kutzner, C.
    MPI Biophys, Theoret & Computat Biophys, Gottingen, Germany..
    Beckmann, A.
    Julich Supercomp Ctr, IAS, Div Math, Julich, Germany..
    Kohnke, B.
    MPI Biophys, Theoret & Computat Biophys, Gottingen, Germany..
    Kabadashow, I.
    Julich Supercomp Ctr, IAS, Div Math, Julich, Germany..
    Dachsel, H.
    Julich Supercomp Ctr, IAS, Div Math, Julich, Germany..
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Grubmueller, H.
    MPI Biophys, Theoret & Computat Biophys, Gottingen, Germany..
    GromEx: Electrostatics with chemical variability for realistic molecular simulations on the exascale2015In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S145-S145Article in journal (Other academic)
  • 7.
    Yoluk, Ozge
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Stockholm, Sweden..
    Orellana, L
    KTH.
    Lindahl, E
    KTH.
    Microsecond time-scale dynamics of the pentameric ligand-gated ion channels: a comparative study2015In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S219-S219Article in journal (Other academic)
  • 8.
    Zander, T.
    et al.
    Helmholtz Zentrum Geesthacht, Geesthacht, Germany..
    Wieland, F.
    Helmholtz Zentrum Geesthacht, Geesthacht, Germany..
    Wang, M
    KTH.
    Raj, A
    KTH.
    Claesson, P
    KTH.
    Dedinaite, A
    KTH.
    Haramus, V.
    Helmholtz Zentrum Geesthacht, Geesthacht, Germany..
    Schreyer, A.
    Helmholtz Zentrum Geesthacht, Geesthacht, Germany..
    Willumeit-Roemer, R.
    Helmholtz Zentrum Geesthacht, Geesthacht, Germany..
    XRR studies of the interaction of DPPC and hyaluronan at high hydrostatic pressure2015In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, p. S137-S137Article in journal (Other academic)
  • 9. Zelenina, M.
    et al.
    Brismar, Hjalmar
    Osmotic water permeability measurements using confocal laser scanning microscopy2000In: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 29, no 3, p. 165-171Article in journal (Refereed)
    Abstract [en]

    We have developed a method for measurement of plasma membrane water permeability (P-f) in intact cells using laser scanning confocal microscopy. The method is based on confocal recording of the fluorescence intensity emitted by calcein-loaded adherent cells during osmotic shock. P-f is calculated as a function of the time constant in the fluorescence intensity change, the cell surface-to-volume ratio and the fractional content of the osmotically active cell volume. The method has been applied to the measurement of water permeability in MDCK cells. The cells behaved as linear osmometers in the interval from 100 to 350 mosM. About 57% of the total cell volume was found to be osmotically inactive. Water movement across the plasma membrane in intact MDCK cells was highly temperature dependent. HgCl2 had no effect on water permeability, while amphotericin B and DMSO significantly increased P-f values. The water permeability in MDCK cells transfected with aquaporin 2 was an order of magnitude higher than in the intact MDCK cell line. The water permeability of the nuclear membrane in both cell lines was found to be unlimited. Thus the intranuclear fluid belongs to the osmotically active portion of the cell. We conclude that the use of confocal microscopy provides a sensitive and reproducible method for measurement of water permeability in different types of adherent cells and potentially for coverslip-attached tissue preparations.

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