Robust Hypothesis Tests for Detecting Statistical Evidence of 2D and 3D Interactions in Single-Molecule Measurements

A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from \emph{in vivo} single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of forces experienced by biomolecules in their native cellular environments. Situations where such forces are biologically relevant range from mitosis to directed transport of protein cargo along cytoskeletal structures. Models commonly applied to quantify single-molecule dynamics assume that effective forces and velocity in the $x,y$ (or $x,y,z$) directions are statistically independent, but this assumption is physically unrealistic in many situations. We present a hypothesis testing approach capable of determining if there is evidence of statistical dependence between positional coordinates in experimentally measured trajectories; if the hypothesis of independence between spatial coordinates is rejected, then a new model accounting for 2D (3D) interactions should be considered to more faithfully represent the underlying experimental kinetics. The technique is robust in the sense that 2D (3D) interactions can be detected via statistical hypothesis testing even if there is substantial inconsistency between the physical particle's actual noise sources and the simplified model's assumed noise structure. For example, 2D (3D) interactions can be reliably detected even if the researcher assumes normal diffusion, but the experimental data experiences "anomalous diffusion" and/or is subjected to a measurement noise characterized by a distribution differing from that assumed by the fitted model. The approach is demonstrated on control simulations and on experimental data (IFT88 directed transport in the primary cilium).Comment: 7 pages, 6 figure

Ultrasonic dispersion (delta V/V) determined from mechanical resonance frequency shifts

With standing wave ultrasonic techniques, small changes in phase velocity which result from changes in some external parameter (e.g., temperature or magnetic field) have traditionally been determined by observing shifts in the mechanical resonance frequency of a composite resonator. Some previous investigators have assumed that the fractional change in velocity is equal to the fractional change in frequency. Substantially improved formulas for determining the dispersion are presented and one of these is shown to be much more accurate than all previous approximations. The results of simulated and actual experiments over wide ranges of dispersion, transducer loading parameter, and frequency are analyzed in order to compare the errors inherent in the various approximations

Two transducer formula for more precise determination of ultrasonic phase velocity from standing wave measurements

A two transducer correction formula valid for both solid and liquid specimens is presented. Using computer simulations of velocity measurements, the accuracy and range of validity of the results are discussed and are compared with previous approximations

Control and coherence of the optical transition of single defect centers in diamond

We demonstrate coherent control of the optical transition of single Nitrogen-Vacancy defect centers in diamond. On applying short resonant laser pulses, we observe optical Rabi oscillations with a half-period as short as 1 nanosecond, an order of magnitude shorter than the spontaneous emission time. By studying the decay of Rabi oscillations, we find that the decoherence is dominated by laser-induced spectral jumps. By using a low-power probe pulse as a detuning sensor and applying post-selection, we demonstrate that spectral diffusion can be overcome in this system to generate coherent photons.Comment: 5 pages,4 figure

Interferometric scattering enables fluorescence-free electrokinetic trapping of single nanoparticles in free solution

Anti-Brownian traps confine single particles in free solution by closed-loop feedback forces that directly counteract Brownian motion. The extended-duration measurement of trapped objects allows detailed characterization of photophysical and transport properties, as well as observation of infrequent or rare dynamics. However, this approach has been generally limited to particles that can be tracked by fluorescent emission. Here we present the Interferometric Scattering Anti-Brownian ELectrokinetic trap (ISABEL trap), which uses interferometric scattering rather than fluorescence to monitor particle position. By decoupling the ability to track (and therefore trap) a particle from collection of its spectroscopic data, the ISABEL trap enables confinement and extended study of single particles that do not fluoresce, that only weakly fluoresce, or which exhibit intermittent fluorescence or photobleaching. This new technique significantly expands the range of nanoscale objects that may be investigated at the single-particle level in free solution.Comment: Manuscript and SI; videos available upon reques

Photoluminescence dispersion as a probe of structural inhomogeneity in silica

We report time-resolved photoluminescence spectra of point defects in amorphous silicon dioxide (silica), in particular the decay kinetics of the emission signals of extrinsic Oxygen Deficient Centres of the second type from singlet and directly-excited triplet states are measured and used as a probe of structural inhomogeneity. Luminescence activity in sapphire ($\alpha$-Al$_2$O$_3$) is studied as well and used as a model system to compare the optical properties of defects in silica with those of defects embedded in a crystalline matrix. Only for defects in silica, we observe a variation of the decay lifetimes with emission energy and a time dependence of the first moment of the emission bands. These features are analyzed within a theoretical model with explicit hypothesis about the effect introduced by the disorder of vitreous systems. Separate estimations of the homogenous and inhomogeneous contributions to the measured emission linewidth are obtained: it is found that inhomogeneous effects strongly condition both the triplet and singlet luminescence activities of oxygen deficient centres in silica, although the degree of inhomogeneity of the triplet emission turns out to be lower than that of the singlet emission. Inhomogeneous effects appear to be negligible in sapphire

Low-frequency noise as a source of dephasing of a qubit

With the growing efforts in isolating solid-state qubits from external decoherence sources, the material-inherent sources of noise start to play crucial role. One representative example is electron traps in the device material or substrate. Electrons can tunnel or hop between a charged and an empty trap, or between a trap and a gate electrode. A single trap typically produces telegraph noise and can hence be modeled as a bistable fluctuator. Since the distribution of hopping rates is exponentially broad, many traps produce flicker-noise with spectrum close to 1/f. Here we develop a theory of decoherence of a qubit in the environment consisting of two-state fluctuators, which experience transitions between their states induced by interaction with thermal bath. Due to interaction with the qubit the fluctuators produce 1/f-noise in the qubit's eigenfrequency. We calculate the results of qubit manipulations - free induction and echo signals - in such environment. The main problem is that in many important cases the relevant random process is both non-Markovian and non-Gaussian. Consequently the results in general cannot be represented by pair correlation function of the qubit eigenfrequency fluctuations. Our calculations are based on analysis of the density matrix of the qubit using methods developed for stochastic differential equations. The proper generating functional is then averaged over different fluctuators using the so-called Holtsmark procedure. The analytical results are compared with simulations allowing checking accuracy of the averaging procedure and evaluating mesoscopic fluctuations. The results allow understanding some observed features of the echo decay in Josephson qubits.Comment: 18 pages, 8 figures, Proc. of NATO/Euresco Conf. "Fundamental Problems of Mesoscopic Physics: Interactions and Decoherence", Granada, Spain, Sept.200

L\'evy Distribution of Single Molecule Line Shape Cumulants in Low Temperature Glass

We investigate the distribution of single molecule line shape cumulants, $\kappa_1,\kappa_2,...$, in low temperature glasses based on the sudden jump, standard tunneling model. We find that the cumulants are described by L\'evy stable laws, thus generalized central limit theorem is applicable for this problem.Comment: 5 pages, 3 figure