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1.	Iarko, V., et al. (författare) Extension of nanoconfined DNA: Quantitative comparison between experiment and theory 2015 Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701- 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.
2.	Alhassid, Y, et al. (författare) Fano interference and cross-section fluctuations in molecular photodissociation 2006 Ingår i: Physical Review A. - 1050-2947. ; 73 Tidskriftsartikel (refereegranskat)abstract We derive an expression for the total photodissociation cross section of a molecule incorporating both direct and indirect processes that proceed through excited resonances, and show that it exhibits generalized Beutler-Fano line shapes. Assuming that the closed system can be modeled by random-matrix theory, we derive the statistical properties of the photodissociation cross section and find that they are significantly affected by the direct processes. In the limit of isolated resonances, we find that direct processes suppress the correlation hole of the cross-section autocorrelation function and lead to a maximum in the cross-section distribution.
3.	Alizadehheidari, Mohammadreza, 1987, et al. (författare) Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics 2015 Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878 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.
4.	Alizadehheidari, Mohammadreza, 1987, et al. (författare) Unfolding of nanoconfined circular DNA 2015 Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1 Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
5.	Almondo, Gino, et al. (författare) Intrinsic viscosity of a suspension of weakly Brownian ellipsoids in shear 2018 Ingår i: Physical Review Fluids. - 2469-990X. ; 3:6 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.
6.	Andersson, Björn, et al. (författare) Advective collisions 2007 Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 80 Tidskriftsartikel (refereegranskat)
7.	Arvedson, Erik, et al. (författare) Staggered ladder spectra. 2006 Ingår i: Physical review letters. - 0031-9007. ; 96:3 Tidskriftsartikel (refereegranskat)abstract We exactly solve a Fokker-Planck equation by determining its eigenvalues and eigenfunctions: we construct nonlinear second-order differential operators which act as raising and lowering operators, generating ladder spectra for the odd- and even-parity states. The ladders are staggered: the odd-even separation differs from even-odd. The Fokker-Planck equation corresponds, in the limit of weak damping, to a generalized Ornstein-Uhlenbeck process where the random force depends upon position as well as time. The process describes damped stochastic acceleration, and exhibits anomalous diffusion at short times and a stationary non-Maxwellian momentum distribution.
8.	Balabanov, Oleksandr, et al. (författare) Bayesian Posterior Approximation With Stochastic Ensembles 2023 Ingår i: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. - 1063-6919. - 9798350301298 ; 2023-June, s. 13701-13711 Konferensbidrag (refereegranskat)abstract We introduce ensembles of stochastic neural networks to approximate the Bayesian posterior, combining stochastic methods such as dropout with deep ensembles. The stochas-tic ensembles are formulated as families of distributions and trained to approximate the Bayesian posterior with variational inference. We implement stochastic ensembles based on Monte Carlo dropout, DropConnect and a novel non-parametric version of dropout and evaluate them on a toy problem and CIFAR image classification. For both tasks, we test the quality of the posteriors directly against Hamil-tonian Monte Carlo simulations. Our results show that stochastic ensembles provide more accurate posterior esti-mates than other popular baselines for Bayesian inference.
9.	Bec, J., et al. (författare) Statistical Models for the Dynamics of Heavy Particles in Turbulence 2024 Ingår i: ANNUAL REVIEW OF FLUID MECHANICS. - 0066-4189 .- 1545-4479. ; 56, s. 189-213 Forskningsöversikt (refereegranskat)abstract When very small particles are suspended in a fluid in motion, they tend to follow the flow. How such tracer particles are mixed, transported, and dispersed by turbulent flow has been successfully described by statistical models. Heavy particles, with mass densities larger than that of the carrying fluid, can detach from the flow. This results in preferential sampling, small-scale fractal clustering, and large relative velocities. To describe these effects of particle inertia, one must consider both particle positions and velocities in phase space. In recent years, statistical phase-space models have significantly contributed to our understanding of inertial-particle dynamics in turbulence. These models help to identify the key mechanisms and nondimensional parameters governing the particle dynamics and have made qualitative and, in some cases, quantitative predictions. This article reviews statistical phase-space models for the dynamics of small, yet heavy, spherical particles in turbulence. We evaluate their effectiveness by comparing their predictions with results from numerical simulations and laboratory experiments, and we summarize their successes and failures.
10.	Bezuglyy, V., et al. (författare) Generalised Ornstein-Uhlenbeck processes 2006 Ingår i: Journal of Mathematical Physics. - : AIP Publishing. - 0022-2488 .- 1089-7658. ; 47 Tidskriftsartikel (refereegranskat)abstract We solve a physically significant extension of a classic problem in the theory of diffusion, namely the Ornstein-Uhlenbeck process [Ornstein and Uhlenbeck, Phys. Rev. 36, 823 (1930)]. Our generalized Ornstein-Uhlenbeck systems include a force which depends upon the position of the particle, as well as upon time. They exhibit anomalous diffusion at short times, and non-Maxwellian velocity distributions in equilibrium. Two approaches are used. Some statistics are obtained from a closed-form expression for the propagator of the Fokker-Planck equation for the case where the particle is initially at rest. In the general case we use spectral decomposition of a Fokker-Planck equation, employing nonlinear creation and annihilation operators to generate the spectrum which consists of two staggered ladders.
11.	Bezuglyy, V., et al. (författare) Poincaré indices of rheoscopic visualisations 2010 Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075. ; 89 Tidskriftsartikel (refereegranskat)abstract Suspensions of small anisotropic particles, "rheoscopic fluids", are used for flow visualisation. By illuminating the fluid with light of three different colours, it is possible to determine Poincaré indices for vector fields formed by the longest axis of the particles. Because this vector field is non-oriented, half-integer Poincaré indices are possible, and are observed experimentally. An exact solution for the direction vector appears to preclude the existence of topological singularities. However, we show that upon averaging over the random initial orientations of particles, singularities with half-integer Poincaré index appear. We describe their normal forms.
12.	Bezuglyy, Vlad, et al. (författare) Universal anomalous diffusion of weakly damped particles 2012 Ingår i: Phys. Rev. E. - 1539-3755. ; 85:6 Tidskriftsartikel (refereegranskat)abstract We show that anomalous diffusion arises in two different models for the motion of randomly forced and weakly damped particles: one is a generalization of the Ornstein-Uhlenbeck process with a random force, which depends on position as well as time, the other is a generalization of the Chandrasekhar-Rosenbluth model of stellar dynamics, encompassing non-Coulombic potentials. We show that both models exhibit anomalous diffusion of position x and momentum p with the same exponents: (x(2)) similar to Cxt(2) and (p(2)) similar to C(p)t(2/5). We are able to determine the prefactors C-x, C-p analytically.
13.	Bhatnagar, Akshay, et al. (författare) Relative velocities in bidisperse turbulent aerosols : Simulations and theory 2018 Ingår i: Physical review. E. - : American Physical Society. - 2470-0045 .- 2470-0053. ; 98:6 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.
14.	Bhowmick, T., et al. (författare) Inertia Induces Strong Orientation Fluctuations of Nonspherical Atmospheric Particles 2024 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 132:3 Tidskriftsartikel (refereegranskat)abstract The orientation of nonspherical particles in the atmosphere, such as volcanic ash and ice crystals, influences their residence times and the radiative properties of the atmosphere. Here, we demonstrate experimentally that the orientation of heavy submillimeter spheroids settling in still air exhibits decaying oscillations, whereas it relaxes monotonically in liquids. Theoretical analysis shows that these oscillations are due to particle inertia, caused by the large particle-fluid mass-density ratio. This effect must be accounted for to model solid particles in the atmosphere.
15.	Borgnino, M., et al. (författare) Alignment of Nonspherical Active Particles in Chaotic Flows 2019 Ingår i: Physical Review Letters. - 0031-9007. ; 123:13 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.
16.	Byron, M., et al. (författare) Shape-dependence of particle rotation in isotropic turbulence 2015 Ingår i: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:3 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.
17.	Cabrera, F., et al. (författare) Experimental validation of fluid inertia models for a cylinder settling in a quiescent flow 2022 Ingår i: Physical Review Fluids. - 2469-990X. ; 7:2 Tidskriftsartikel (refereegranskat)abstract The precise description of the motion of anisotropic particles in a flow rests on the understanding of the force and torque acting on them. Here, we study experimentally small, very elongated particles settling in a fluid at small Reynolds number. In our experiments, we can, to a very good approximation, relate the rate of rotation of cylindrical tungsten rods, of aspect ratios = 8 and = 16, settling in pure glycerol, to the torque they are experiencing. This allows us to compare the measured torque with expressions obtained either in the slender-rod limit or in the case of spheroids. Both theories predict a simple angle dependence for the torque, which is found to capture very well the experimental results. The slender-rod theory overestimates the results for the two aspect ratios considered, while the expression obtained for a spheroid provides a better approximation for = 16. Comparing our results with those of previous experiments provides further insight on the conditions of validity of the slender-rod theory. The translational dynamics is shown to be in qualitative agreement with the slender-rod and spheroid models, the former one being found to represent better the experimental data.
18.	Candelier, Fabien, et al. (författare) Angular Dynamics of a Small Particle in Turbulence 2016 Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117 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.
19.	Candelier, F., et al. (författare) Inertial torque on a squirmer 2022 Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 953 Tidskriftsartikel (refereegranskat)abstract A small spheroid settling in a quiescent fluid experiences an inertial torque that aligns it so that it settles with its broad side first. Here we show that an active particle experiences such a torque too, as it settles in a fluid at rest. For a spherical squirmer, the torque is T '=-9/8m(f)(v(s)((0) )boolean AND v(g)((0))) where v(s)((0) )is the swimming velocity, v(g)((0)) is the settling velocity in the Stokes approximation and mf is the equivalent fluid mass. This torque aligns the swimming direction against gravity: swimming up is stable, swimming down is unstable.
20.	Candelier, F., et al. (författare) Role of inertia for the rotation of a nearly spherical particle in a general linear flow 2015 Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 91:5 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.
21.	Candelier, F., et al. (författare) Second-order inertial forces and torques on a sphere in a viscous steady linear flow 2023 Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 954 Tidskriftsartikel (refereegranskat)abstract We compute the full set of second-order inertial corrections to the instantaneous force and torque acting on a small spherical rigid particle moving unsteadily in a general steady linear flow. This is achieved by using matched asymptotic expansions and formulating the problem in a coordinate system co-moving with the background flow. Effects of unsteadiness and fluid-velocity gradients are assumed to be small, but to dominate in the far field over those of the velocity difference between the body and fluid, making the results essentially relevant to weakly positively or negatively buoyant particles. The outer solution (which at first order is responsible for the Basset-Boussinesq history force at short time and for shear-induced forces such as the Saffman lift force at long time) is expressed via a flow-dependent tensorial kernel. The second-order inner solution brings a number of different contributions to the force and torque. Some are proportional to the relative translational or angular acceleration between the particle and fluid, while others take the form of products of the rotation/strain rate of the background flow and the relative translational or angular velocity between the particle and fluid. Adding the outer and inner contributions, the known added-mass force or the spin-induced lift force are recovered, and new effects involving the velocity gradients of the background flow are revealed. The resulting force and torque equations provide a rational extension of the classical Basset-Boussinesq-Oseen equation incorporating all first- and second-order fluid inertia effects resulting from both unsteadiness and velocity gradients of the carrying flow.
22.	Candelier, F., et al. (författare) Settling of an asymmetric dumbbell in a quiescent fluid 2016 Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 802, s. 174-185 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.
23.	Candelier, F., et al. (författare) Time-dependent lift and drag on a rigid body in a viscous steady linear flow 2019 Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 864, s. 554-595 Tidskriftsartikel (refereegranskat)abstract We compute the leading-order inertial corrections to the instantaneous force acting on a rigid body moving with a time-dependent slip velocity in a linear flow field, assuming that the square root of the Reynolds number based on the fluid-velocity gradient is much larger than the Reynolds number based on the slip velocity between the body and the fluid. As a first step towards applications to dilute sheared suspensions and turbulent particle-laden flows, we seek a formulation allowing this force to be determined for an arbitrarily shaped body moving in a general linear flow. We express the equations governing the flow disturbance in a non-orthogonal coordinate system moving with the undisturbed flow and solve the problem using matched asymptotic expansions. The use of the co-moving coordinates enables the leading-order inertial corrections to the force to be obtained at any time in an arbitrary linear flow field. We then specialize this approach to compute the time-dependent force components for a sphere moving in three canonical flows: solid-body rotation, planar elongation, and uniform shear. We discuss the behaviour and physical origin of the different force components in the short-time and quasi-steady limits. Last, we illustrate the influence of time-dependent and quasi-steady inertial effects by examining the sedimentation of prolate and oblate spheroids in a pure shear flow.
24.	Cedenblad, Lukas, et al. (författare) Planetesimals on Eccentric Orbits Erode Rapidly 2021 Ingår i: Astrophysical Journal. - : American Astronomical Society. - 0004-637X .- 1538-4357. ; 921:2 Tidskriftsartikel (refereegranskat)abstract We investigate the possibility of erosion of planetesimals in a protoplanetary disk. We use theory and direct numerical simulations (lattice Boltzmann method) to calculate the erosion of large-much larger than the mean-free path of gas molecules-bodies of different shapes in flows. We find that erosion follows a universal power law in time, at intermediate times, independent of the Reynolds number of the flow and the initial shape of the body. Consequently, we estimate that planetesimals in eccentric orbits, of even very small eccentricity, rapidly (in about 100 yr) erodes away if the semimajor axis of their orbit lies in the inner disk-less than about 10 au. Even planetesimals in circular orbits erode away in approximately 10,000 yr if the semimajor axis of their orbits are <0.6 au.
25.	Cichos, F., et al. (författare) Machine learning for active matter 2020 Ingår i: Nature Machine Intelligence. - : Springer Science and Business Media LLC. - 2522-5839. ; 2:2, s. 94-103 Tidskriftsartikel (refereegranskat)abstract The availability of large datasets has boosted the application of machine learning in many fields and is now starting to shape active-matter research as well. Machine learning techniques have already been successfully applied to active-matter data-for example, deep neural networks to analyse images and track objects, and recurrent nets and random forests to analyse time series. Yet machine learning can also help to disentangle the complexity of biological active matter, helping, for example, to establish a relation between genetic code and emergent bacterial behaviour, to find navigation strategies in complex environments, and to map physical cues to animal behaviours. In this Review, we highlight the current state of the art in the application of machine learning to active matter and discuss opportunities and challenges that are emerging. We also emphasize how active matter and machine learning can work together for mutual benefit. This Review surveys machine learning techniques that are currently developed for a range of research topics in biological and artificial active matter and also discusses challenges and exciting opportunities. This research direction promises to help disentangle the complexity of active matter and gain fundamental insights for instance in collective behaviour of systems at many length scales from colonies of bacteria to animal flocks.
26.	Collins, D., et al. (författare) Lord Kelvin's isotropic helicoid 2021 Ingår i: Physical Review Fluids. - 2469-990X. ; 6:7 Tidskriftsartikel (refereegranskat)abstract Nearly 150 years ago, Lord Kelvin proposed the isotropic helicoid, a particle with isotropic yet chiral interactions with a fluid so that translation couples to rotation. An implementation of his design fabricated with a three-dimensional printer is found experimentally to have no detectable translation-rotation coupling, although the particle point-group symmetry allows this coupling. We explain these results by demonstrating that in Stokes flow, the chiral coupling of such isotropic helicoids made out of nonchiral vanes is due only to hydrodynamic interactions between these vanes. Therefore it is small. In summary, Kelvin's predicted isotropic helicoid exists, but only as a weak breaking of a symmetry of noninteracting vanes in Stokes flow.
27.	Cui, Z., et al. (författare) Alignment statistics of rods with the Lagrangian stretching direction in a channel flow 2020 Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 901 Tidskriftsartikel (refereegranskat)abstract In homogeneous isotropic turbulence, slender rods are known to align with the Lagrangian stretching direction. However, how the degree of alignment depends on the aspect ratio of the rod is not understood. Moreover, particle-laden flows are often anisotropic and inhomogeneous. Therefore we study the alignment of rods with the Lagrangian stretching direction in a channel flow, which is approximately homogeneous and isotropic near the centre but inhomogeneous and anisotropic near the walls. Our main question is how the distribution of relative angles between a rod and the Lagrangian stretching direction depends on the aspect ratio of the rod and upon the distance of the rod from the channel wall. We find that this distribution exhibits two regimes: a plateau at small angles corresponding to random uncorrelated motion, and power-law tails due to large excursions. We find that slender rods near the channel centre align better with the Lagrangian stretching direction compared with those near the channel wall. These observations are explained in terms of simple statistical models based on Jeffery's equation, qualitatively near the channel centre and quantitatively near the channel wall. Lastly we discuss the consequences of our results for the distribution of relative angles between the orientations of nearby rods (Zhao et al., Phys. Rev. Fluids, vol. 4, 2019, 054602).
28.	Dilthey, Stefan, et al. (författare) Classical phase-space analysis of vibronically coupled systems 2002 Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606. ; 116, s. 69-78 Tidskriftsartikel (refereegranskat)
29.	Dittrich, Thomas, et al. (författare) Spectral signatures of chaotic diffusion in systems with and without spatial disorder 2001 Ingår i: Physica E. - 1386-9477. ; 9, s. 494-497 Annan publikation (övrigt vetenskapligt/konstnärligt)
30.	Dubey, Anshuman, et al. (författare) Bifurcations in droplet collisions 2022 Ingår i: Physical Review Fluids. - 2469-990X. ; 7:6 Tidskriftsartikel (refereegranskat)abstract Saffman and Turner [P. G. Saffman and J. S. Turner, J. Fluid Mech. 1, 16 (1956)] argued that the collision rate for droplets in turbulence increases as the turbulent strain rate increases. However, the numerical simulations of Dhanasekaran et al. [J. Dhanasekaran et al., J. Fluid Mech. 910, A10 (2021)] in a steady straining flow showed that the Saffman-Turner model is oversimplified because it neglects droplet-droplet interactions. These result in a complex dependence of the collision rate on the strain rate and on the differential settling speed. Here we show that this dependence is explained by a sequence of bifurcations in the collision dynamics. We compute the bifurcation diagram when strain is aligned with gravity and show that it yields important insights into the collision dynamics. First, the steady-state collision rate remains nonzero in the limit Kn -> 0, contrary to the common assumption that the collision rate tends to zero in this limit (Kn is a nondimensional measure of the mean free path of air). Second, the nonmonotonic dependence of the collision rate on the differential settling speed is explained by a grazing bifurcation. Third, the bifurcation analysis explains why so-called closed trajectories appear and disappear. Fourth, our analysis predicts strong spatial clustering near certain saddle points, where the effects of strain and differential settling cancel.
31.	Dubey, Anshuman, et al. (författare) Fractal dimensions and trajectory crossings in correlated random walks 2018 Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 98 Tidskriftsartikel (refereegranskat)abstract © 2018 American Physical Society. We study spatial clustering in a discrete-time, one-dimensional, stochastic, toy model of heavy particles in turbulence and calculate the spectrum of multifractal dimensions Dq as functions of a dimensionless parameter, α, that plays the role of an inertia parameter. Using the fact that it suffices to consider the linearized dynamics of the model at small separations, we find that Dq=D2/(q-1) for q=2,3,. The correlation dimension D2 turns out to be a nonanalytic function of the inertia parameter in this model. We calculate D2 for small α up to the next-to-leading order in the nonanalytic term.
32.	Duncan, Kevin, et al. (författare) Clustering by mixing flows. 2005 Ingår i: Physical review letters. - 0031-9007. ; 95:24 Tidskriftsartikel (refereegranskat)abstract We calculate the Lyapunov exponents for particles suspended in a random three-dimensional flow, concentrating on the limit where the viscous damping rate is small compared to the inverse correlation time. In this limit Lyapunov exponents are obtained as a power series in epsilon, a dimensionless measure of the particle inertia. Although the perturbation generates an asymptotic series, we obtain accurate results from a Padé-Borel summation. Our results prove that particles suspended in an incompressible random mixing flow can show pronounced clustering when the Stokes number is large and we characterize two distinct clustering effects which occur in that limit.
33.	Einarsson, Jonas, et al. (författare) Effect of weak fluid inertia upon Jeffery orbits 2015 Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 91 Tidskriftsartikel (refereegranskat)abstract We consider the rotation of small neutrally buoyant axisymmetric particles in a viscous steady shear flow. When inertial effects are negligible the problem exhibits infinitely many periodic solutions, the “Jeffery orbits.” We compute how inertial effects lift their degeneracy by perturbatively solving the coupled particle-flow equations. We obtain an equation of motion valid at small shear Reynolds numbers, for spheroidal particles with arbitrary aspect ratios. We analyze how the linear stability of the “log-rolling” orbit depends on particle shape and find it to be unstable for prolate spheroids. This resolves a puzzle in the interpretation of direct numerical simulations of the problem. In general, both unsteady and nonlinear terms in the Navier-Stokes equations are important.
34.	Einarsson, Jonas, et al. (författare) Orientational dynamics of weakly inertial axisymmetric particles in steady viscous flows 2014 Ingår i: Physica D : Non-linear phenomena. - : Elsevier BV. - 0167-2789. ; 278, s. 79-85 Tidskriftsartikel (refereegranskat)abstract The orientational dynamics of weakly inertial axisymmetric particles in a steady flow is investigated. We derive an asymptotic equation of motion for the unit axial vector along the particle symmetry axis, valid for small Stokes number St, and for any axisymmetric particle in any steady linear viscous flow. This reduced dynamics is analysed in two ways, both pertain to the case of a simple shear flow. In this case inertia induces a coupling between precession and nutation. This coupling affects the dynamics of the particle, breaks the degeneracy of the Jeffery orbits, and creates two limiting periodic orbits. We calculate the leading-order Floquet exponents of the limiting periodic orbits and show analytically that prolate objects tend to a tumbling orbit, while oblate objects tend to a log-rolling orbit, in agreement with previous analytical and numerical results. Second, we analyse the role of the limiting orbits when rotational noise is present. We formulate the Fokker-Planck equation describing the orientational distribution of an axisymmetric particle, valid for small St and general Peclet number Pe. Numerical solutions of the Fokker-Planck equation, obtained by means of expansion in spherical harmonics, show that stationary orientational distributions are close to the inertia-free case when PeSt << 1, whereas they are determined by inertial effects, though small, when Pe >> 1/St >> 1. (C) 2014 The Authors. Published by Elsevier B.V.
35.	Einarsson, Jonas, et al. (författare) Periodic and aperiodic tumbling of microrods advected in a microchannel flow 2013 Ingår i: Acta Mechanica. - : Springer Science and Business Media LLC. - 0001-5970 .- 1619-6937. ; 224:10, s. 2281-2289 Tidskriftsartikel (refereegranskat)abstract We report on an experimental investigation of the tumbling of microrods in the shear flow of a microchannel (dimensions: 40 mm x 2.5 mm x 0.4 mm. The rods are 20-30 mu m long and their diameters are of the order of 1 mu m. Images of the centre-of-mass motion and the orientational dynamics of the rods are recorded using a microscope equipped with a CCD camera. A motorised microscope stage is used to track individual rods as they move along the channel. Automated image analysis determines the position and orientation of a tracked rod in each video frame. We find different behaviours, depending on the particle shape, its initial position, and orientation. First, we observe periodic as well as aperiodic tumbling. Second, the data show that different tumbling trajectories exhibit different sensitivities to external perturbations. These observations can be explained by slight asymmetries of the rods. Third, we observe that after some time, initially periodic trajectories lose their phase. We attribute this to drift of the centre of mass of the rod from one to another streamline of the channel flow.
36.	Einarsson, Jonas, et al. (författare) Rotation of a spheroid in a simple shear at small Reynolds number 2015 Ingår i: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 27:6 Tidskriftsartikel (refereegranskat)abstract We derive an effective equation of motion for the orientational dynamics of a neutrally buoyant spheroid suspended in a simple shear flow, valid for arbitrary particle aspect ratios and to linear order in the shear Reynolds number.We show how inertial effects lift the degeneracy of the Jeffery orbits and determine the stabilities of the log-rolling and tumbling orbits at infinitesimal shear Reynolds numbers. For prolate spheroids, we find stable tumbling in the shear plane and log-rolling is unstable. For oblate spheroids, by contrast, log-rolling is stable and tumbling is unstable provided that the particle is not too disk-like (moderate asphericity). For very flat oblate spheroids, both log-rolling and tumbling are stable, separated by an unstable limit cycle.
37.	Einarsson, Jonas, et al. (författare) Spherical particle sedimenting in weakly viscoelastic shear flow 2017 Ingår i: Physical Review Fluids. - 2469-990X. ; 2:6 Tidskriftsartikel (refereegranskat)abstract We consider the dynamics of a small spherical particle driven through an unbounded viscoelastic shear flow by an external force. We give analytical solutions to both the mobility problem (the velocity of a forced particle) and the resistance problem (the force on a fixed particle), valid to second order in the dimensionless Deborah and Weissenberg numbers, which represent the elastic relaxation time of the fluid relative to the rate of translation and the imposed shear rate. We find a shear-induced lift at O(Wi), a modified drag at O(De(2)) and O(Wi(2)), and a second lift that is orthogonal to the first, at O(Wi(2)). The relative importance of these effects depends strongly on the orientation of the forcing relative to the shear. We discuss how these forces affect the terminal settling velocity in an inclined shear flow. We also describe a basis set of symmetric Cartesian tensors and demonstrate how they enable general tensorial perturbation calculations such as the present theory. In particular, this scheme allows us to write down a solution to the inhomogeneous Stokes equations, required by the perturbation expansion, by a sequence of algebraic manipulations well suited to computer implementation.
38.	Einarsson, Jonas, et al. (författare) Tumbling of asymmetric microrods in a microchannel flow 2016 Ingår i: Physics of Fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 28:1 Tidskriftsartikel (refereegranskat)abstract We describe results of measurements of the orientational motion of glass microrods in a microchannel flow, following the orientational motion of particles with different shapes. We determine how the orientational dynamics depends on the shape of the particle and on its initial orientation. We find that the dynamics depends so sensitively on the degree to which particle axisymmetry is broken that it is difficult to find particles that are sufficiently axisymmetric so that they exhibit periodic tumbling ("Jeffery orbits"). The results of our measurements confirm earlier theoretical analysis predicting sensitive dependence on particle shape and its initial orientation. Our results illustrate the different types of orientational dynamics for asymmetric particles predicted by theory.
39.	Elias Wolff, Federico, et al. (författare) How Levins’ dynamics emerges from a Ricker metapopulation model 2016 Ingår i: Theoretical Ecology. - : Springer Science and Business Media LLC. - 1874-1738 .- 1874-1746. ; 9:2, s. 173-183 Tidskriftsartikel (refereegranskat)abstract Understanding the dynamics of metapopulations close to extinction is of vital importance for management. Levins-like models, in which local patches are treated as either occupied or empty, have been used extensively to explore the extinction dynamics of metapopulations, but they ignore the important role of local population dynamics. In this paper, we consider a stochastic metapopulation model where local populations follow a stochastic, density-dependent dynamics (the Ricker model), and use this framework to investigate the behaviour of the metapopulation on the brink of extinction. We determine under which circumstances the metapopulation follows a time evolution consistent with Levins’ dynamics. We derive analytical expressions for the colonisation and extinction rates (c and e) in Levins-type models in terms of reproduction, survival and dispersal parameters of the local populations, providing an avenue to parameterising Levins-like models from the type of information on local demography that is available for a number of species. To facilitate applying our results, we provide a numerical algorithm for computing c and e.
40.	Eriksson, Anders, 1975, et al. (författare) An accurate model for genetic hitchhiking 2008 Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 178:1, s. 439-451 Tidskriftsartikel (refereegranskat)abstract We suggest a simple deterministic approximation for the growth of the favored-allele frequency during a selective sweep. Using this approximation we introduce an accurate model for genetic hitchhiking. Only when Ns < 10 (N is the population size and s denotes the selection coefficient) are discrepancies between our approximation and direct numerical simulations of a Moran model notable. Our model describes the gene genealogies of a contiguous segment of neutral loci close to the selected one, and it does not assume that the selective sweep happens instantaneously. This enables us to compute SNP distributions on the neutral segment without bias.
41.	Eriksson, Anders, 1975, et al. (författare) Gene-history correlation and population structure. 2004 Ingår i: Physical biology. - : IOP Publishing. - 1478-3967 .- 1478-3975. ; 1:3-4, s. 220-8 Tidskriftsartikel (refereegranskat)abstract Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.
42.	Eriksson, Anders, 1975, et al. (författare) Metapopulation dynamics on the brink of extinction 2013 Ingår i: Theoretical Population Biology. - : Elsevier BV. - 0040-5809. ; 83, s. 101-122 Tidskriftsartikel (refereegranskat)abstract We analyse metapopulation dynamics in terms of an individual-based, stochastic model of a finite metapopulation. We suggest a new approach, using the number of patches in the population as a large parameter. This approach does not require that the number of individuals per patch is large, neither is it necessary to assume a time-scale separation between local population dynamics and migration. Our approach makes it possible to accurately describe the dynamics of metapopulations consisting of many small patches. We focus on metapopulations on the brink of extinction. We estimate the time to extinction and describe the most likely path to extinction. We find that the logarithm of the time to extinction is proportional to the product of two vectors, a vector characterising the distribution of patch population sizes in the quasi-steady state, and a vector–related to Fisher’s reproduction vector–that quantifies the sensitivity of the quasi-steady state distribution to demographic fluctuations. We compare our analytical results to stochastic simulations of the model, and discuss the range of validity of the analytical expressions. By identifying fast and slow degrees of freedom in the metapopulation dynamics, we show that the dynamics of large metapopulations close to extinction is approximately described by a deterministic equation originally proposed by Levins (1969). We were able to compute the rates in Levins’ equation in terms of the parameters of our stochastic, individual-based model. It turns out, however, that the interpretation of the dynamical variable depends strongly on the intrinsic growth rate and carrying capacity of the patches. Only when the local growth rate and the carrying capacity are large does the slow variable correspond to the number of patches, as envisaged by Levins. Last but not least, we discuss how our findings relate to other, widely used metapopulation models.
43.	Eriksson, Anders, 1975, et al. (författare) Multiple paternity: determining the minimum number of sires of a large brood 2010 Ingår i: Molecular Ecology Resources. - 1755-098X. ; 10:2, s. 282-291 Tidskriftsartikel (refereegranskat)abstract We describe an efficient algorithm for determining exactly the minimum number of sires consistent with the multi-locus genotypes of a mother and her progeny. We consider cases where a simple exhaustive search through all possible sets of sires is impossible in practice because it would take too long to complete. Our algorithm for solving this combinatorial optimization problem avoids visiting large parts of search space that would not result in a solution with fewer sires. This improvement is of particular importance when the number of allelic types in the progeny array is large and when the minimum number of sires is expected to be large. Precisely in such cases, it is important to know the minimum number of sires: this number gives an exact bound on the most likely number of sires estimated by a random search algorithm in a parameter region where it may be difficult to determine whether it has converged. We apply our algorithm to data from the marine snail, Littorina saxatilis.
44.	Eriksson, Anders, 1975, et al. (författare) On the effect of fluctuating recombination rates on the decorrelation of gene histories in the human genome. 2005 Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 169:2, s. 1175-8 Tidskriftsartikel (refereegranskat)abstract We show how to incorporate fluctuations of the recombination rate along the chromosome into standard gene-genealogical models for the decorrelation of gene histories. This enables us to determine how small-scale fluctuations (Poissonian hot-spot model) and large-scale variations (Kong et al. 2002) of the recombination rate influence this decorrelation. We find that the empirically determined large-scale variations of the recombination rate give rise to a significantly slower decay of correlations compared to the standard, unstructured gene-genealogical model assuming constant recombination rate. A model with long-range recombination-rate variations and with demographic structure (divergent population) is found to be consistent with the empirically observed slow decorrelation of gene histories. Conversely, we show that small-scale recombination-rate fluctuations do not alter the large-scale decorrelation of gene histories.
45.	Eriksson, Anders, 1975, et al. (författare) On the statistics of selectively neutral variation 2002 Ingår i: Physical Review E. - 1539-3755. ; 65 Tidskriftsartikel (refereegranskat)
46.	Eriksson, Anders, 1975, et al. (författare) Sequential Markov coalescent algorithms for population models with demographic structure. 2009 Ingår i: Theoretical population biology. - : Elsevier BV. - 1096-0325 .- 0040-5809. ; 76:2, s. 84-91 Tidskriftsartikel (refereegranskat)abstract We analyse sequential Markov coalescent algorithms for populations with demographic structure: for a bottleneck model, a population-divergence model, and for a two-island model with migration. The sequential Markov coalescent method is an approximation to the coalescent suggested by McVean and Cardin, and by Marjoram and Wall. Within this algorithm we compute, for two individuals randomly sampled from the population, the correlation between times to the most recent common ancestor and the linkage probability corresponding to two different loci with recombination rate R between them. These quantities characterise the linkage between the two loci in question. We find that the sequential Markov coalescent method approximates the coalescent well in general in models with demographic structure. An exception is the case where individuals are sampled from populations separated by reduced gene flow. In this situation, the correlations may be significantly underestimated. We explain why this is the case.
47.	Eriksson, Anders, 1975, et al. (författare) The emergence of the rescue effect from explicit within- and between-patch dynamics in a metapopulation 2014 Ingår i: Proceedings of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8452 .- 1471-2954. ; 281:1780 Tidskriftsartikel (refereegranskat)abstract Immigration can rescue local populations from extinction, helping to stabilise a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic parameters and the rescue effect at the metapopulation level has received very little attention by modellers. We develop an analytical framework that allows us to describe the emergence of the rescue effect from interacting local stochastic dynamics. We show this framework to be applicable to a wide range of spatial scales, providing a powerful and convenient alternative to individual‐based models for making predictions concerning the fate of metapopulations. We show that the rescue effect plays an important role in minimising the increase in local extinction probability associated with high demographic stochasticity, but its role is more limited in the case of high local environmental stochasticity of recruitment or survival. While most models postulate the rescue effect, our framework provides an explicit mechanistic link between local dynamics and the emergence of the rescue effect, and more generally the stability of the whole metapopulation.
48.	Eriksson, Anders, 1975, et al. (författare) The total branch length of sample genealogies in populations of variable size 2010 Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 186:2, s. 601-611 Tidskriftsartikel (refereegranskat)abstract We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we study the distribution of the total branch lengths of its sample genealogies. Within the coalescent approximation we have obtained a general expression— Equation 20—for the moments of this distribution with a given arbitrary dependence of the population size on time. We investigate how the frequency of population-size variations alters the total branch length.
49.	Fornander, Louise, 1984, et al. (författare) Using nanofluidic channels to probe dynamics of RAD51-Filaments 2015 Ingår i: 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. - 9780979806476 ; , s. 1826-1828 Konferensbidrag (refereegranskat)abstract Using nanochannels, passivated with a lipid bilayer to avoid sticking of proteins, we study Rad51 filaments bound to single- and double stranded DNA. We demonstrate how we can discern different properties of the filaments by studying them at different degrees of confinement. Unlike the bacterial homologue RecA, that forms homogeneous filaments along DNA, Rad51 forms heterogeneous filaments containing both rigid kinks as well as flexible regions. Varying the counterion, the DNA substrate as well as the initial protein concentration, we try to understand the factors governing the structure of the filaments.
50.	Fornander, Louise, 1984, et al. (författare) Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels 2016 Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 32:33, s. 8403-8412 Tidskriftsartikel (refereegranskat)abstract RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg2+ or Ca2+), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes.

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