| 1. |
- Hammar, Petter, et al.
(författare)
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The lac repressor displays facilitated diffusion in living cells
- 2012
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 336:6088, s. 1595-1598
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Tidskriftsartikel (refereegranskat)abstract
- Transcription factors (TFs) are proteins that regulate the expression of genes by binding sequence-specific sites on the chromosome. It has been proposed that to find these sites fast and accurately, TFs combine one-dimensional (1D) sliding on DNA with 3D diffusion in the cytoplasm. This facilitated diffusion mechanism has been demonstrated in vitro, but it has not been shown experimentally to be exploited in living cells. We have developed a single-molecule assay that allows us to investigate the sliding process in living bacteria. Here we show that the lac repressor slides 45 ± 10 base pairs on chromosomal DNA and that sliding can be obstructed by other DNA-bound proteins near the operator. Furthermore, the repressor frequently (>90%) slides over its natural lacO(1) operator several times before binding. This suggests a trade-off between rapid search on nonspecific sequences and fast binding at the specific sequence.
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| 2. |
- Marklund, Erik G., et al.
(författare)
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Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:49, s. 19796-19801
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Tidskriftsartikel (refereegranskat)abstract
- Transcription factors search for specific operator sequences by alternating rounds of 3D diffusion with rounds of 1D diffusion (sliding) along the DNA. The details of such sliding have largely been beyond direct experimental observation. For this purpose we devised an analytical formulation of umbrella sampling along a helical coordinate, and from extensive and fully atomistic simulations we quantified the free-energy landscapes that underlie the sliding dynamics and dissociation kinetics for the LacI dimer. The resulting potential of mean force distributions show a fine structure with an amplitude of 1 k(B)T for sliding and 12 kBT for dissociation. Based on the free-energy calculations the repressor slides in close contact with DNA for 8 bp on average before making a microscopic dissociation. By combining the microscopic molecular-dynamics calculations with Brownian simulation including rotational diffusion from the microscopically dissociated state we estimate a macroscopic residence time of 48 ms at the same DNA segment and an in vitro sliding distance of 240 bp. The sliding distance is in agreement with previous in vitro sliding-length estimates. The in vitro prediction for the macroscopic residence time also compares favorably to what we measure by single-molecule imaging of nonspecifically bound fluorescently labeled LacI in living cells. The investigation adds to our understanding of transcription-factor search kinetics and connects the macro-/mesoscopic rate constants to the microscopic dynamics.
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| 3. |
- Bashinov, A. V., et al.
(författare)
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Electron acceleration and emission in a field of a plane and converging dipole wave of relativistic amplitudes with the radiation reaction force taken into account
- 2013
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Ingår i: Quantum electronics (Woodbury, N.Y.). - 1063-7818 .- 1468-4799. ; 43:4, s. 291-299
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Tidskriftsartikel (refereegranskat)abstract
- A comparative analysis is performed of the electron emission characteristics as the electrons move in laser fields with ultra-relativistic intensity and different configurations corresponding to a plane or tightly focused wave. For a plane travelling wave, analytical expressions are derived for the emission characteristics, and it is shown that the angular distribution of the radiation intensity changes qualitatively even when the wave intensity is much less than that in the case of the radiation-dominated regime. An important conclusion is drawn that the electrons in a travelling wave tend to synchronised motion under the radiation reaction force. The characteristic features of the motion of electrons are found in a converging dipole wave, associated with the curvature of the phase front and nonuniformity of the field distribution. The values of the maximum achievable longitudinal momenta of electrons accelerated to the centre, as well as their distribution function are determined. The existence of quasi-periodic trajectories near the focal region of the dipole wave is shown, and the characteristics of the emission of both accelerated and oscillating electrons are analysed.
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| 4. |
- Berthomier, M., et al.
(författare)
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Alfven : magnetosphere-ionosphere connection explorers
- 2012
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Ingår i: Experimental astronomy. - Dordrecht : Springer. - 0922-6435 .- 1572-9508. ; 33:2-3, s. 445-489
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Tidskriftsartikel (refereegranskat)abstract
- The aurorae are dynamic, luminous displays that grace the night skies of Earth's high latitude regions. The solar wind emanating from the Sun is their ultimate energy source, but the chain of plasma physical processes leading to auroral displays is complex. The special conditions at the interface between the solar wind-driven magnetosphere and the ionospheric environment at the top of Earth's atmosphere play a central role. In this Auroral Acceleration Region (AAR) persistent electric fields directed along the magnetic field accelerate magnetospheric electrons to the high energies needed to excite luminosity when they hit the atmosphere. The "ideal magnetohydrodynamics" description of space plasmas which is useful in much of the magnetosphere cannot be used to understand the AAR. The AAR has been studied by a small number of single spacecraft missions which revealed an environment rich in wave-particle interactions, plasma turbulence, and nonlinear acceleration processes, acting on a variety of spatio-temporal scales. The pioneering 4-spacecraft Cluster magnetospheric research mission is now fortuitously visiting the AAR, but its particle instruments are too slow to allow resolve many of the key plasma physics phenomena. The Alfv,n concept is designed specifically to take the next step in studying the aurora, by making the crucial high-time resolution, multi-scale measurements in the AAR, needed to address the key science questions of auroral plasma physics. The new knowledge that the mission will produce will find application in studies of the Sun, the processes that accelerate the solar wind and that produce aurora on other planets.
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| 5. |
- Breed, Martin, 1981-, et al.
(författare)
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Pollen diversity matters : revealing the neglected effect of pollen diversity on fitness in fragmented landscapes
- 2012
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 21:24, s. 5955-5968
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Tidskriftsartikel (refereegranskat)abstract
- Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that individual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen diversity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.
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| 6. |
- Brodin, G., et al.
(författare)
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Particle-in-cell simulations of electron spin effects in plasmas
- 2013
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Ingår i: Journal of Plasma Physics. - : Cambridge University Press (CUP). - 0022-3778 .- 1469-7807. ; 79:4, s. 377-382
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Tidskriftsartikel (refereegranskat)abstract
- We present a particle-in-cell code accounting for the magnetic dipole force and for the magnetization currents associated with the electron spin. The electrons are divided into spin-up and spin-down populations relative to the magnetic field, where the magnetic dipole force acts in opposite directions for the two species. To validate the code, we study wakefield generation by an electromagnetic pulse propagating parallel to an external magnetic field. The properties of the generated wakefield are shown to be in good agreement with previous theoretical results. Generalizations of the code to account for other quantum effects are discussed.
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| 7. |
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| 8. |
- Gonoskov, Arkady, et al.
(författare)
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Anomalous radiative trapping in laser fields of extreme intensity
- 2014
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Ingår i: Physical Review Letters. - : American Physical Society. - 0031-9007 .- 1079-7114. ; 113, s. 014801-
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate that charged particles in a suciently intense standing wave are compressed toward, and oscillate synchronously at, the antinodes of the electric eld. We call this unusualbehaviour `anomalous radiative trapping' (ART). We show using dipole pulses, which oer a pathto increased laser intensity, that ART opens up new possibilities for the generation of radiationand particle beams, both of which are high-energy, directed and collimated. ART also provides a mechanism for particle control in high-intensity quantum-electrodynamics experiments.
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| 9. |
- Gonoskov, Arkady, et al.
(författare)
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Probing Nonperturbative QED with Optimally Focused Laser Pulses
- 2013
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 111:6
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Tidskriftsartikel (refereegranskat)abstract
- We study nonperturbative pair production in intense, focused laser fields called e-dipole pulses. We address the conditions required, such as the quality of the vacuum, for reaching high intensities without initiating beam-depleting cascades, the number of pairs which can be created, and experimental detection of the created pairs. We find that e-dipole pulses offer an optimal method of investigating nonperturbative QED.
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| 10. |
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