| 1. |
- Iarko, V., et al.
(författare)
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Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
- 2015
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701-
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Tidskriftsartikel (refereegranskat)abstract
- The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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| 2. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Tidskriftsartikel (refereegranskat)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Unfolding of nanoconfined circular DNA
- 2015
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Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Almondo, Gino, et al.
(författare)
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Intrinsic viscosity of a suspension of weakly Brownian ellipsoids in shear
- 2018
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Ingår i: Physical Review Fluids. - 2469-990X. ; 3:6
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the angular dynamics of triaxial ellipsoids in a shear flow subject to weak thermal noise. By numerically integrating an overdamped angular Langevin equation, we find the steady angular probability distribution for a range of triaxial particle shapes. From this distribution we compute the intrinsic viscosity of a dilute suspension of triaxial particles. We determine how the viscosity depends on particle shape in the limit of weak thermal noise. While the deterministic angular dynamics depends very sensitively on particle shape, we find that the shape dependence of the intrinsic viscosity is weaker, in general, and that suspensions of rodlike particles are the most sensitive to breaking of axisymmetry. The intrinsic viscosity of a dilute suspension of triaxial particles is smaller than that of a suspension of axisymmetric particles with the same volume and the same ratio of major to minor axis lengths.
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| 5. |
- Bhatnagar, Akshay, et al.
(författare)
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Relative velocities in bidisperse turbulent aerosols : Simulations and theory
- 2018
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Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 98:6
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Tidskriftsartikel (refereegranskat)abstract
- We perform direct numerical simulations of a bidisperse suspension of heavy spherical particles in forced, homogeneous, and isotropic three-dimensional turbulence. We compute the joint distribution of relative particle distances and longitudinal relative velocities between particles of different inertia. For a pair of particles with small difference in their inertias we compare our results with recent theoretical predictions [Meibohm et al., Phys. Rev. E 96, 061102 (2017)] for the shape of this distribution. We also compute the moments of relative velocities as a function of particle separation and compare with the theoretical predictions. We observe good agreement. For a pair of particles that are very different from each other-one is heavy and the other one has negligible inertia-we give a theory to calculate their root-mean-square relative velocity. This theory also agrees well with the results of our simulations.
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| 6. |
- Borgnino, M., et al.
(författare)
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Alignment of Nonspherical Active Particles in Chaotic Flows
- 2019
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Ingår i: Physical Review Letters. - 0031-9007. ; 123:13
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Tidskriftsartikel (refereegranskat)abstract
- We study the orientation statistics of spheroidal, axisymmetric microswimmers, with shapes ranging from disks to rods, swimming in chaotic, moderately turbulent flows. Numerical simulations show that rodlike active particles preferentially align with the flow velocity. To explain the underlying mechanism, we solve a statistical model via the perturbation theory. We show that such an alignment is caused by correlations of fluid velocity and its gradients along particle paths combined with fore-aft symmetry breaking due to both swimming and particle nonsphericity. Remarkably, the discovered alignment is found to be a robust kinematical effect, independent of the underlying flow evolution. We discuss its possible relevance for aquatic ecology.
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| 7. |
- Byron, M., et al.
(författare)
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Shape-dependence of particle rotation in isotropic turbulence
- 2015
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Ingår i: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:3
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Tidskriftsartikel (refereegranskat)abstract
- We consider the rotation of neutrally buoyant axisymmetric particles suspended in isotropic turbulence. Using laboratory experiments as well as numerical and analytical calculations, we explore how particle rotation depends upon particle shape. We find that shape strongly affects orientational trajectories, but that it has negligible effect on the variance of the particle angular velocity. Previous work has shown that shape significantly affects the variance of the tumbling rate of axisymmetric particles. It follows that shape affects the spinning rate in away that is, on average, complementary to the shape-dependence of the tumbling rate. We confirm this relationship using direct numerical simulations, showing how tumbling rate and spinning rate variances show complementary trends for rod-shaped and disk-shaped particles. We also consider a random but non-turbulent flow. This allows us to explore which of the features observed for rotation in turbulent flow are due to the effects of particle alignment in vortex tubes. (C) 2015 AIP Publishing LLC.
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| 8. |
- Candelier, Fabien, et al.
(författare)
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Angular Dynamics of a Small Particle in Turbulence
- 2016
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117
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Tidskriftsartikel (refereegranskat)abstract
- We compute the angular dynamics of a neutrally buoyant nearly spherical particle immersed in an unsteady fluid. We assume that the particle is small, that its translational slip velocity is negligible, and that unsteady and convective inertia are small perturbations. We derive an approximation for the torque on the particle that determines the first inertial corrections to Jeffery’s equation. These corrections arise as a consequence of local vortex stretching and can be substantial in turbulence, where local vortex stretching is strong and closely linked to the irreversibility of turbulence.
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| 9. |
- Candelier, F., et al.
(författare)
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Role of inertia for the rotation of a nearly spherical particle in a general linear flow
- 2015
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 91:5
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the angular dynamics of a neutrally buoyant, nearly spherical particle immersed in a steady general linear flow. The hydrodynamic torque acting on the particle is obtained by means of a reciprocal theorem, a regular perturbation theory exploiting the small eccentricity of the nearly spherical particle, and by assuming that inertial effects are small but finite.
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| 10. |
- Candelier, F., et al.
(författare)
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Settling of an asymmetric dumbbell in a quiescent fluid
- 2016
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 802, s. 174-185
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Tidskriftsartikel (refereegranskat)abstract
- We compute the hydrodynamic torque on a dumbbell (two spheres linked by a massless rigid rod) settling in a quiescent fluid at small but finite Reynolds number. The spheres have the same mass densities but different sizes. When the sizes are quite different, the dumbbell settles vertically, aligned with the direction of gravity, the largest sphere first. But when the size difference is sufficiently small, then its steady-state angle is determined by a competition between the size difference and the Reynolds number. When the sizes of the spheres are exactly equal, then fluid inertia causes the dumbbell to settle in a horizontal orientation.
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