Swimmer-tracer scattering at low Reynolds number

Understanding the stochastic dynamics of tracer particles in active fluids is important for identifying the physical properties of flow generating objects such as colloids, bacteria or algae. Here, we study both analytically and numerically the scattering of a tracer particle in different types of time-dependent, hydrodynamic flow fields. Specifically, we compare the tracer motion induced by an externally driven colloid with the one generated by various self-motile, multi-sphere swimmers. Our results suggest that force-free swimmers generically induce loop-shaped tracer trajectories. The specific topological structure of these loops is determined by the hydrodynamic properties of the microswimmer. Quantitative estimates for typical experimental conditions imply that the loops survive on average even if Brownian motion effects are taken into account.Comment: 14 pages, to appear in Soft Matte

The development of a systematic ultrasound protocol facilitates the visualization of foreign bodies within the canine distal limb

Ultrasonography is an excellent investigative tool that can assist with the diagnosis of soft tissue conditions. In human medicine, ultrasonography is a fundamental diagnostic tool for the investigation of suspected vegetal foreign bodies (VFB), with protocol-based ultrasonography providing increased accuracy compared to lesion-focused examinations. Protocol-based ultrasonography is an emerging tool within the veterinary field, however, compared to human medicine is not routinely employed. The objective of this study was to develop a systematic ultrasound protocol to examine the distal limb for the visualization of vegetal foreign bodies (SUEDVEG). A 12 MHz linear and an 18 MHz high-frequency small-footprint linear array transducer was used on cadaver forelimbs (n = 6) and hindlimbs (n = 6) with images obtained from three common foreign body locations within the distal limb; 1; the interdigital webbing, 2; the palmar/plantar aspect of the phalanges and metacarpus and 3; the dorsal region of the phalanges and metacarpus. From these images, a 13-step systematic musculoskeletal protocol was developed and utilized on eight clinical cases or 10 limbs that had signs typical of distal limb VFB to preliminarily validate the proposed method. Vegetal foreign bodies were successfully identified and retrieved in seven (n = 8) clinical cases with method steps 9 and 11 (orthogonal views) identifying the majority of VFBs. The described ultrasound method appears highly useful for visualizing soft tissue locations of the canine distal limb known for tracking foreign bodies. Further studies are required to validate the described systematic examination method as the preferred clinical protocol over currently used lesion-focused exploration techniques

Electrophoresis of positioned nucleosomes

We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as wrapped length of DNA on the electrophoretic mobility of the complex. The predictions of the model are in qualitative agreement with experimental results on mononucleosomes assembled on short DNA fragments (<400bp). Influence of additional experimental parameters like gel concentration, ionic strength, effective charges is also discussed in the framework of the model, and is found to be qualitatively consistent with experiments when available. Based on the present model, we propose a simple semi-empirical formula describing positioning of nucleosomes as seen through electrophoresis.Comment: to appear in Biophys. J. 29 page

Low Reynolds number hydrodynamics of asymmetric, oscillating dumbbell pairs

Active dumbbell suspensions constitute one of the simplest model system for collective swimming at low Reynolds number. Generalizing recent work, we derive and analyze stroke-averaged equations of motion that capture the effective hydrodynamic far-field interaction between two oscillating, asymmetric dumbbells in three space dimensions. Time-averaged equations of motion, as those presented in this paper, not only yield a considerable speed-up in numerical simulations, they may also serve as a starting point when deriving continuum equations for the macroscopic dynamics of multi-swimmer suspensions. The specific model discussed here appears to be particularly useful in this context, since it allows one to investigate how the collective macroscopic behavior is affected by changes in the microscopic symmetry of individual swimmers.Comment: 10 pages, to appear in EPJ Special Topic

Dumbbell transport and deflection in a spatially periodic potential

We present theoretical results on the deterministic and stochastic motion of a dumbbell carried by a uniform flow through a three-dimensional spatially periodic potential. Depending on parameters like the flow velocity, there are two different kinds of movement: transport along a potential valley and stair-like motion oblique to the potential trenches. The crossover between these two regimes, as well as the deflection angle, depends on the size of the dumbbell. Moreover, thermal fluctuations cause a resonance-like variation in the deflection angle as a function of the dumbbell extension.Comment: 5 pages, 8 figure

Stochastic Eulerian Lagrangian Methods for Fluid-Structure Interactions with Thermal Fluctuations

We present approaches for the study of fluid-structure interactions subject to thermal fluctuations. A mixed mechanical description is utilized combining Eulerian and Lagrangian reference frames. We establish general conditions for operators coupling these descriptions. Stochastic driving fields for the formalism are derived using principles from statistical mechanics. The stochastic differential equations of the formalism are found to exhibit significant stiffness in some physical regimes. To cope with this issue, we derive reduced stochastic differential equations for several physical regimes. We also present stochastic numerical methods for each regime to approximate the fluid-structure dynamics and to generate efficiently the required stochastic driving fields. To validate the methodology in each regime, we perform analysis of the invariant probability distribution of the stochastic dynamics of the fluid-structure formalism. We compare this analysis with results from statistical mechanics. To further demonstrate the applicability of the methodology, we perform computational studies for spherical particles having translational and rotational degrees of freedom. We compare these studies with results from fluid mechanics. The presented approach provides for fluid-structure systems a set of rather general computational methods for treating consistently structure mechanics, hydrodynamic coupling, and thermal fluctuations.Comment: 24 pages, 3 figure

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

Influence of Hydrodynamic Interactions on Mechanical Unfolding of Proteins

We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds. Hydrodynamic interactions are also shown to facilitate unfolding at constant force and inhibit stretching by fluid flows.Comment: to be published in Journal of Physics: Condensed Matte