Two-Dimensional Flow Nanometry of Biological Nanoparticles for Accurate Determination of Their Size and Emission Intensity

Biological nanoparticles (BNPs) are of high interest due to their key role in various biological processes and use as biomarkers. BNP size and molecular composition are decisive for their functions, but simultaneous determination of both properties with high accuracy remains challenging, which is a severe limitation. Surface-sensitive microscopy allows one to precisely determine fluorescence or scattering intensity, but not the size of individual BNPs. The latter is better determined by tracking their random motion in bulk, but the limited illumination volume for tracking this motion impedes reliable intensity determination. We here show that attaching BNPs (specifically, vesicles and functionalized gold NPs) to a supported lipid bilayer, subjecting them to a hydrodynamic flow, and tracking their motion via surface-sensitive imaging enable to determine their diffusion coefficients and flow-induced drift velocities and to accurately quantify both BNP size and emission intensity. For vesicles, the high accuracy is demonstrated by resolving the expected radius-squared dependence of their fluorescence intensity.Comment: 28 pages, 5 figure

Slipping friction of an optically and magnetically manipulated microsphere rolling at a glass-water interface

The motion of submerged magnetic microspheres rolling at a glass-water interface has been studied using magnetic rotation and optical tweezers combined with bright-field microscopy particle tracking techniques. Individual microspheres of varying surface roughness were magnetically rotated both in and out of an optical trap to induce rolling, along either plain glass cover slides or glass cover slides functionalized with polyethylene glycol. It has been observed that the manipulated microspheres exhibited nonlinear dynamic rolling-while-slipping motion characterized by two motional regimes: At low rotational frequencies, the speed of microspheres free-rolling along the surface increased proportionately with magnetic rotation rate; however, a further increase in the rotation frequency beyond a certain threshold revealed a sharp transition to a motion in which the microspheres slipped with respect to the external magnetic field resulting in decreased rolling speeds. The effects of surface-microsphere interactions on the position of this threshold frequency are posed and investigated. Similar experiments with microspheres rolling while slipping in an optical trap showed congruent results.Comment: submitted to Journal of Applied Physics, 11 figure

Dynamics of Attention in Depth: Evidence from Mutli-Element Tracking

The allocation of attention in depth is examined using a multi-element tracking paradigm. Observers are required to track a predefined subset of from two to eight elements in displays containing up to sixteen identical moving elements. We first show that depth cues, such as binocular disparity and occlusion through T-junctions, improve performance in a multi-element tracking task in the case where element boundaries are allowed to intersect in the depiction of motion in a single fronto-parallel plane. We also show that the allocation of attention across two perceptually distinguishable planar surfaces either fronto-parallel or receding at a slanting angle and defined by coplanar elements, is easier than allocation of attention within a single surface. The same result was not found when attention was required to be deployed across items of two color populations rather than of a single color. Our results suggest that, when surface information does not suffice to distinguish between targets and distractors that are embedded in these surfaces, division of attention across two surfaces aids in tracking moving targets.National Science Foundation (IRI-94-01659); Office of Naval Research (N00014-95-1-0409, N00014-95-1-0657

Time persistency of floating particle clusters in free-surface turbulence

We study the dispersion of light particles floating on a flat shear-free surface of an open channel in which the flow is turbulent. This configuration mimics the motion of buoyant matter (e.g. phytoplankton, pollutants or nutrients) in water bodies when surface waves and ripples are smooth or absent. We perform direct numerical simulation of turbulence coupled with Lagrangian particle tracking, considering different values of the shear Reynolds number (Re{\tau} = 171 and 509) and of the Stokes number (0.06 < St < 1 in viscous units). Results show that particle buoyancy induces clusters that evolve towards a long-term fractal distribution in a time much longer than the Lagrangian integral fluid time scale, indicating that such clusters over-live the surface turbulent structures which produced them. We quantify cluster dynamics, crucial when modeling dispersion in free-surface flow turbulence, via the time evolution of the cluster correlation dimension

Learning Task Constraints from Demonstration for Hybrid Force/Position Control

We present a novel method for learning hybrid force/position control from demonstration. We learn a dynamic constraint frame aligned to the direction of desired force using Cartesian Dynamic Movement Primitives. In contrast to approaches that utilize a fixed constraint frame, our approach easily accommodates tasks with rapidly changing task constraints over time. We activate only one degree of freedom for force control at any given time, ensuring motion is always possible orthogonal to the direction of desired force. Since we utilize demonstrated forces to learn the constraint frame, we are able to compensate for forces not detected by methods that learn only from the demonstrated kinematic motion, such as frictional forces between the end-effector and the contact surface. We additionally propose novel extensions to the Dynamic Movement Primitive (DMP) framework that encourage robust transition from free-space motion to in-contact motion in spite of environment uncertainty. We incorporate force feedback and a dynamically shifting goal to reduce forces applied to the environment and retain stable contact while enabling force control. Our methods exhibit low impact forces on contact and low steady-state tracking error.Comment: Under revie

Probing DNA conformational changes with high temporal resolution by Tethered Particle Motion

The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA molecule and detecting changes of its amplitude of movement. We discuss in this context the time resolution of TPM, which strongly depends on the particle-DNA complex relaxation time, i.e. the characteristic time it takes to explore its configuration space by diffusion. By comparing theory, simulations and experiments, we propose a calibration of TPM at the dynamical level: we analyze how the relaxation time grows with both DNA contour length (from 401 to 2080 base pairs) and particle radius (from 20 to 150~nm). Notably we demonstrate that, for a particle of radius 20~nm or less, the hydrodynamic friction induced by the particle and the surface does not significantly slow down the DNA. This enables us to determine the optimal time resolution of TPM in distinct experimental contexts which can be as short as 20~ms.Comment: Improved version, to appear in Physical Biology. 10 pages + 10 pages of supporting materia

Quasi full-disk maps of solar horizontal velocities using SDO/HMI data

For the first time, the motion of granules (solar plasma on the surface on scales larger than 2.5 Mm) has been followed over the entire visible surface of the Sun, using SDO/HMI white-light data. Horizontal velocity fields are derived from image correlation tracking using a new version of the coherent structure tracking algorithm.The spatial and temporal resolutions of the horizontal velocity map are 2.5 Mm and 30 min respectively . From this reconstruction, using the multi-resolution analysis, one can obtain to the velocity field at different scales with its derivatives such as the horizontal divergence or the vertical component of the vorticity. The intrinsic error on the velocity is ~0.25 km/s for a time sequence of 30 minutes and a mesh size of 2.5 Mm.This is acceptable compared to the granule velocities, which range between 0.3 km/s and 1.8 km/s. A high correlation between velocities computed from Hinode and SDO/HMI has been found (85%). From the data we derive the power spectrum of the supergranulation horizontal velocity field, the solar differential rotation, and the meridional velocity.Comment: 8 pages, 11 figures, accepted in Astronomy and Astrophysic

Kassiopeia: A Modern, Extensible C++ Particle Tracking Package

The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle tracking simulations which targets experiments containing complex geometries and electromagnetic fields, with high priority put on calculation efficiency, customizability, extensibility, and ease of use for novice programmers. To solve Kassiopeia's target physics problem the software is capable of simulating particle trajectories governed by arbitrarily complex differential equations of motion, continuous physics processes that may in part be modeled as terms perturbing that equation of motion, stochastic processes that occur in flight such as bulk scattering and decay, and stochastic surface processes occuring at interfaces, including transmission and reflection effects. This entire set of computations takes place against the backdrop of a rich geometry package which serves a variety of roles, including initialization of electromagnetic field simulations and the support of state-dependent algorithm-swapping and behavioral changes as a particle's state evolves. Thanks to the very general approach taken by Kassiopeia it can be used by other experiments facing similar challenges when calculating particle trajectories in electromagnetic fields. It is publicly available at https://github.com/KATRIN-Experiment/Kassiopei