Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification

Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary 'blinking' without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation

Numerical constraints on the model of stochastic excitation of solar-type oscillations

Analyses of a 3D simulation of the upper layers of a solar convective envelope provide constraints on the physical quantities which enter the theoretical formulation of a stochastic excitation model of solar p modes, for instance the convective velocities and the turbulent kinetic energy spectrum. These constraints are then used to compute the acoustic excitation rate for solar p modes, P. The resulting values are found ~5 times larger than the values resulting from a computation in which convective velocities and entropy fluctuations are obtained with a 1D solar envelope model built with the time-dependent, nonlocal Gough (1977) extension of the mixing length formulation for convection (GMLT). This difference is mainly due to the assumed mean anisotropy properties of the velocity field in the excitation region. The 3D simulation suggests much larger horizontal velocities compared to vertical ones than in the 1D GMLT solar model. The values of P obtained with the 3D simulation constraints however are still too small compared with the values inferred from solar observations. Improvements in the description of the turbulent kinetic energy spectrum and its depth dependence yield further increased theoretical values of P which bring them closer to the observations. It is also found that the source of excitation arising from the advection of the turbulent fluctuations of entropy by the turbulent movements contributes ~ 65-75 % to the excitation and therefore remains dominant over the Reynolds stress contribution. The derived theoretical values of P obtained with the 3D simulation constraints remain smaller by a factor ~3 compared with the solar observations. This shows that the stochastic excitation model still needs to be improved.Comment: 11 pages, 9 figures, accepted for publication in A&

Non-perturbative flow equations from continuous unitary transformations

We use a novel parameterization of the flowing Hamiltonian to show that the flow equations based on continuous unitary transformations, as proposed by Wegner, can be implemented through a nonlinear partial differential equation involving one flow parameter and two system specific auxiliary variables. The implementation is non-perturbative as the partial differential equation involves a systematic expansion in fluctuations, controlled by the size of the system, rather than the coupling constant. The method is applied to the Lipkin model to construct a mapping which maps the non-interacting spectrum onto the interacting spectrum to a very high accuracy. This function is universal in the sense that the full spectrum for any (large) number of particles can be obtained from it. In a similar way expectation values for a large class of operators can be obtained, which also makes it possible to probe the stucture of the eigenstates.Comment: 24 pages, 13 figure

Solar Oscillations and Convection: II. Excitation of Radial Oscillations

Solar p-mode oscillations are excited by the work of stochastic, non-adiabatic, pressure fluctuations on the compressive modes. We evaluate the expression for the radial mode excitation rate derived by Nordlund and Stein (Paper I) using numerical simulations of near surface solar convection. We first apply this expression to the three radial modes of the simulation and obtain good agreement between the predicted excitation rate and the actual mode damping rates as determined from their energies and the widths of their resolved spectral profiles. We then apply this expression for the mode excitation rate to the solar modes and obtain excellent agreement with the low l damping rates determined from GOLF data. Excitation occurs close to the surface, mainly in the intergranular lanes and near the boundaries of granules (where turbulence and radiative cooling are large). The non-adiabatic pressure fluctuations near the surface are produced by small instantaneous local imbalances between the divergence of the radiative and convective fluxes near the solar surface. Below the surface, the non-adiabatic pressure fluctuations are produced primarily by turbulent pressure fluctuations (Reynolds stresses). The frequency dependence of the mode excitation is due to effects of the mode structure and the pressure fluctuation spectrum. Excitation is small at low frequencies due to mode properties -- the mode compression decreases and the mode mass increases at low frequency. Excitation is small at high frequencies due to the pressure fluctuation spectrum -- pressure fluctuations become small at high frequencies because they are due to convection which is a long time scale phenomena compared to the dominant p-mode periods.Comment: Accepted for publication in ApJ (scheduled for Dec 10, 2000 issue). 17 pages, 27 figures, some with reduced resolution -- high resolution versions available at http://www.astro.ku.dk/~aake/astro-ph/0008048

Empirical evidence for the Birch and Swinnerton-Dyer conjectures for modular jacobians of genus 2 curves

This paper provides empirical evidence for the Birch and Swinnerton-Dyer conjectures for modular Jacobians of genus 2 curves. The second of these conjectures relates six quantities associated to a Jacobian over the rational numbers. One of these six quantities is the size of the Shafarevich-Tate group. Unable to compute that, we computed the five other quantities and solved for the last one. In all 32 cases, the result is very close to an integer that is a power of 2. In addition, this power of 2 agrees with the size of the 2-torsion of the Shafarevich-Tate group, which we could compute

Solar Flux Emergence Simulations

We simulate the rise through the upper convection zone and emergence through the solar surface of initially uniform, untwisted, horizontal magnetic flux with the same entropy as the non-magnetic plasma that is advected into a domain 48 Mm wide from from 20 Mm deep. The magnetic field is advected upward by the diverging upflows and pulled down in the downdrafts, which produces a hierarchy of loop like structures of increasingly smaller scale as the surface is approached. There are significant differences between the behavior of fields of 10 kG and 20 or 40 kG strength at 20 Mm depth. The 10 kG fields have little effect on the convective flows and show little magnetic buoyancy effects, reaching the surface in the typical fluid rise time from 20 Mm depth of 32 hours. 20 and 40 kG fields significantly modify the convective flows, leading to long thin cells of ascending fluid aligned with the magnetic field and their magnetic buoyancy makes them rise to the surface faster than the fluid rise time. The 20 kG field produces a large scale magnetic loop that as it emerges through the surface leads to the formation of a bipolar pore-like structure.Comment: Solar Physics (in press), 12 pages, 13 figur

Magnetohydrodynamic turbulence in warped accretion discs

Warped, precessing accretion discs appear in a range of astrophysical systems, for instance the X-ray binary Her X-1 and in the active nucleus of NGC4258. In a warped accretion disc there are horizontal pressure gradients that drive an epicyclic motion. We have studied the interaction of this epicyclic motion with the magnetohydrodynamic turbulence in numerical simulations. We find that the turbulent stress acting on the epicyclic motion is comparable in size to the stress that drives the accretion, however an important ingredient in the damping of the epicyclic motion is its parametric decay into inertial waves.Comment: to appear in the proceedings of the 20th Texas Symposium on Relativistic Astrophysics, J. C. Wheeler & H. Martel (eds.