Improved localization precision via restricting confined biomolecule stochastic motion in single-molecule localization microscopy

Single-molecule localization microscopy (SMLM) plays an irreplaceable role in biological studies, in which nanometer-sized biomolecules are hardly to be resolved due to diffraction limit unless being stochastically activated and accurately located by SMLM. For biological samples preimmobilized for SMLM, most biomolecules are cross-linked and constrained at their immobilizing sites but still expected to undergo confined stochastic motion in regard to their nanometer sizes. However, few lines of direct evidence have been reported about the detectability and influence of confined biomolecule stochastic motion on localization precision in SMLM. Here, we access the potential stochastic motion for each immobilized single biomolecule by calculating the displacements between any two of its localizations at different frames during sequential imaging of Alexa Fluor-647-conjugated oligonucleotides. For most molecules, localization displacements are remarkably larger at random frame intervals than at shortest intervals even after sample drift correction, increase with interval times and then saturate, showing that biomolecule stochastic motion is detected and confined around the immobilizing sizes in SMLM. Moreover, localization precision is inversely proportional to confined biomolecule stochastic motion, whereas it can be deteriorated or improved by enlarging the biomolecules or adding a post-crosslinking step, respectively. Consistently, post-crosslinking of cell samples sparsely stained for tubulin proteins results in a better localization precision. Overall, this study reveals that confined stochastic motion of immobilized biomolecules worsens localization precision in SMLM, and improved localization precision can be achieved via restricting such a motion.

First passage dynamics of stochastic motion in heterogeneous media driven by correlated white Gaussian and coloured non-Gaussian noises

We study the first passage dynamics for a diffusing particle experiencing a spatially varying diffusion coefficient while driven by correlated additive Gaussian white noise and multiplicative coloured non-Gaussian noise. We consider three functional forms for position dependence of the diffusion coefficient: power-law, exponential, and logarithmic. The coloured non-Gaussian noise is distributed according to Tsallis' $q$-distribution. Tracks of the non-Markovian systems are numerically simulated by using the fourth-order Runge-Kutta algorithm and the first passage times are recorded. The first passage time density is determined along with the mean first passage time. Effects of the noise intensity and self-correlation of the multiplicative noise, the intensity of the additive noise, the cross-correlation strength, and the non-extensivity parameter on the mean first passage time are discussed.

The control effort to steer self-propelled microswimmers depends on their morphology: comparing symmetric spherical versus asymmetric L -shaped particles

Active goal-directed motion requires real-time adjustment of control signals depending on the system’s status, also known as control. The amount of information that needs to be processed depends on the desired motion and control, and on the system’s morphology. The morphology of the system may directly effectuate or support the desired motion. This morphology-based reduction to the neuronal ‘control effort’ can be quantified by a novel information-entropy-based approach. Here, we apply this novel measure of ‘control effort’ to active microswimmers of different morphology. Their motion is a combination of directed deterministic and stochastic motion. In spherical microswimmers, the active propulsion leads to linear velocities. Active propulsion of asymmetric L -shaped particles leads to circular or—on tilted substrates—directed motion. Thus, the difference in shape, i.e. the morphology of the particles, directly influence the motion. Here, we quantify how this morphology can be exploited by control schemes for the purpose of steering the particles towards targets. Using computer simulations, we found in both cases a significantly lower control effort for L -shaped particles. However, certain movements can only be achieved by spherical particles. This demonstrates that a suitably designed microswimmer’s morphology might be exploited to perform specific tasks.

Confined Electrochemical Behaviors of Single Platinum Nanoparticles Revealing Ultrahigh Density of Gas Molecules inside a Nanobubble

Understanding the basic physicochemical properties of gas molecules confined within nanobubbles is of fundamental importance for chemical and biological process. Here we successfully monitored the nanobubble-confined electrochemical behaviors of single platinum nanoparticles (PtNPs) at a carbon fiber ultramicroelectrode in HClO4 and H2O2 solution. Owing to the catalytic decomposition of H2O2, a single oxygen nanobubble formed on individual PtNPs to block the active surface of particle for proton reduction and suppress their stochastic motion, resulting in significantly distinguished current traces. Furthermore, the combination of theoretical calculation and high-resolution electrochemical measurement allowed the size of nanobubble and the oxygen gas density inside a single nanobubble to be quantified. And the ultrahigh oxygen density inside (9286 kg/m3) was revealed, indicating gas molecules in a nanosized space existed with a high state of aggregation. Our approach sheds light on gas aggregation behaviors of nanoscale bubbles using single-entity electrochemical measurement.

Phenomenology of quantum turbulence in superfluid helium

Quantum turbulence—the stochastic motion of quantum fluids such as 4He and 3He-B, which display pure superfluidity at zero temperature and two-fluid behavior at finite but low temperatures—has been a subject of intense experimental, theoretical, and numerical studies over the last half a century. Yet, there does not exist a satisfactory phenomenological framework that captures the rich variety of experimental observations, physical properties, and characteristic features, at the same level of detail as incompressible turbulence in conventional viscous fluids. Here we present such a phenomenology that captures in simple terms many known features and regimes of quantum turbulence, in both the limit of zero temperature and the temperature range of two-fluid behavior.

Study of Wound Healing Dynamics by Single Pseudo-Particle Tracking in Phase Contrast Images Acquired in Time-Lapse

Cellular contacts modify the way cells migrate in a cohesive group with respect to a free single cell. The resulting motion is persistent and correlated, with cells’ velocities self-aligning in time. The presence of a dense agglomerate of cells makes the application of single particle tracking techniques to define cells dynamics difficult, especially in the case of phase contrast images. Here, we propose an original pipeline for the analysis of phase contrast images of the wound healing scratch assay acquired in time-lapse, with the aim of extracting single particle trajectories describing the dynamics of the wound closure. In such an approach, the membrane of the cells at the border of the wound is taken as a unicum, i.e., the wound edge, and the dynamics is described by the stochastic motion of an ensemble of points on such a membrane, i.e., pseudo-particles. For each single frame, the pipeline of analysis includes: first, a texture classification for separating the background from the cells and for identifying the wound edge; second, the computation of the coordinates of the ensemble of pseudo-particles, chosen to be uniformly distributed along the length of the wound edge. We show the results of this method applied to a glioma cell line (T98G) performing a wound healing scratch assay without external stimuli. We discuss the efficiency of the method to assess cell motility and possible applications to other experimental layouts, such as single cell motion. The pipeline is developed in the Python language and is available upon request.