White Rabbit Precision Time Protocol on Long-Distance Fiber Links.

The application of White Rabbit precision time protocol (WR-PTP) in long-distance optical fiber links has been investigated. WR-PTP is an implementation of PTP in synchronous Ethernet optical fiber networks, originally intended for synchronization of equipment within a range of 10 km. This paper discusses the results and limitations of two implementations of WR-PTP in the existing communication fiber networks. A 950-km WR-PTP link was realized using unidirectional paths in a fiber pair between Espoo and Kajaani, Finland. The time transfer on this link was compared (after initial calibration) against a clock comparison by GPS precise point positioning (PPP). The agreement between the two methods remained within [Formula: see text] over three months of measurements. Another WR-PTP implementation was realized between Delft and Amsterdam, the Netherlands, by cascading two links of 137 km each. In this case, the WR links were realized as bidirectional paths in single fibers. The measured time offset between the starting and end points of the link was within 5 ns with an uncertainty of 8 ns, mainly due to the estimated delay asymmetry caused by chromatic dispersion.

Frequency-comb-referenced tunable diode laser spectroscopy and laser stabilization applied to laser cooling.

Laser cooling of trapped atoms and ions in optical clocks demands stable light sources with precisely known absolute frequencies. Since a frequency comb is a vital part of any optical clock, the comb lines can be used for stabilizing tunable, user-friendly diode lasers. Here, a light source for laser cooling of trapped strontium ions is described. The megahertz-level stability and absolute frequency required are realized by stabilizing a distributed-feedback semiconductor laser to a frequency comb. Simple electronics is used to lock and scan the laser across the comb lines, and comb mode number ambiguities are resolved by using a separate, saturated absorption cell that exhibits easily distinguishable hyperfine absorption lines with known frequencies. Due to the simplicity, speed, and wide tuning range it offers, the employed technique could find wider use in precision spectroscopy.

Optical tweezers reveal force plateau and internal friction in PEG-induced DNA condensation.

The simplified artificial environments in which highly complex biological systems are studied do not represent the crowded, dense, salty, and dynamic environment inside the living cell. Consequently, it is important to investigate the effect of crowding agents on DNA. We used a dual-trap optical tweezers instrument to perform force spectroscopy experiments at pull speeds ranging from 0.3 to 270 µm/s on single dsDNA molecules in the presence of poly(ethylene glycol) (PEG) and monovalent salt. PEG of sizes 1,500 and 4,000 Da condensed DNA, and force-extension data contained a force plateau at approximately 1 pN. The level of the force plateau increased with increasing pull speed. During slow pulling the dissipated work increased linearly with pull speed. The calculated friction coefficient did not depend on amount of DNA incorporated in the condensate, indicating internal friction is independent of the condensate size. PEG300 had no effect on the dsDNA force-extension curve. The force plateau implies that condensation induced by crowding agents resembles condensation induced by multivalent cations.

Dual-trap optical tweezers with real-time force clamp control.

Single molecule force clamp experiments are widely used to investigate how enzymes, molecular motors, and other molecular mechanisms work. We developed a dual-trap optical tweezers instrument with real-time (200 kHz update rate) force clamp control that can exert 0-100 pN forces on trapped beads. A model for force clamp experiments in the dumbbell-geometry is presented. We observe good agreement between predicted and observed power spectra of bead position and force fluctuations. The model can be used to predict and optimize the dynamics of real-time force clamp optical tweezers instruments. The results from a proof-of-principle experiment in which lambda exonuclease converts a double-stranded DNA tether, held at constant tension, into its single-stranded form, show that the developed instrument is suitable for experiments in single molecule biology.

Principal component analysis detects sleepiness-related changes in balance control.

Computerized posturography exploits balance scores that quantify the size, dynamics, or structure of the recorded sway. Since people employ different balance strategies, one single balance score will not detect balance changes in all subjects. Principal component analysis (PCA) can combine balance scores that quantify different features into one new balance score. We tested the score with 20 subjects by measuring their balance every 2 h during 28 h of sustained waking. The new balance score was more sensitive than its components (p<0.001 vs. p≥0.051) to the small sleepiness-related balance decrements that occurred during the short 28-h period. PCA provided a more sensitive balance score that applied to all of the subjects.

Step length measurement--theory and simulation for tethered bead constant-force single molecule assay.

Linear molecular motors translocate along polymeric tracks using discrete steps. The step length is usually measured using constant-force single molecule experiments in which the polymer is tethered to a force-clamped microsphere. During the enzymatic cycle the motor shortens the tether contour length. Experimental conditions influence the achievable step length resolution, and ideally experiments should be conducted with high clamp-force using slow motors linked to small beads via stiff short tethers. We focus on the limitations that the polymer-track flexibility, the thermal motion of the microsphere, and the motor kinetics pose for step-length measurement in a typical optical tweezers experiment. An expression for the signal/noise ratio in a constant-force, worm-like chain tethered particle, single-molecule experiment is developed. The signal/noise ratio is related to the Fourier transform of the pairwise distance distribution, commonly used to determine step length from a time-series. Monte Carlo simulations verify the proposed theory for experimental parameter values typically encountered with molecular motors (polymerases and helicases) translocating along single- or double-stranded nucleic acids. The predictions are consistent with recent experimental results for double-stranded DNA tethers. Our results map favorable experimental conditions for observing single motor steps on various substrates but indicate that principal resolution limits are set by thermal fluctuations.

Evaluating sleepiness using force platform posturography.

We have investigated the feasibility to use posturography as a method to estimate sleep deprivation. This manuscript presents a proof-of-concept of this idea. Twenty-one healthy subjects aged 20-37 years participated in the study. The subjects were deprived of sleep for up to 36 h. Their postural stability was measured as a function of sleep deprivation time. As a reference the critical fusion frequency method for measuring sleepiness was used. The 163 posturographic parameters used for analyzing the posturographic data were found from the literature. Of these parameters, the fractal dimension of the sway path, the most common frequency of the sway, the time-interval for open-loop control of stance, and the most common amplitude of the sway showed the highest linear correlations with sleep deprivation time. Using these four parameters we were able to estimate the sleep deprivation time with an accuracy better than 5 h for 80% of the subjects.