Spectral rate theory for projected two-state kinetics

Classical rate theories often fail in cases where the observable(s) or order parameter(s) used are poor reaction coordinates or the observed signal is deteriorated by noise, such that no clear separation between reactants and products is possible. Here, we present a general spectral two-state rate theory for ergodic dynamical systems in thermal equilibrium that explicitly takes into account how the system is observed. The theory allows the systematic estimation errors made by standard rate theories to be understood and quantified. We also elucidate the connection of spectral rate theory with the popular Markov state modeling (MSM) approach for molecular simulation studies. An optimal rate estimator is formulated that gives robust and unbiased results even for poor reaction coordinates and can be applied to both computer simulations and single-molecule experiments. No definition of a dividing surface is required. Another result of the theory is a model-free definition of the reaction coordinate quality (RCQ). The RCQ can be bounded from below by the directly computable observation quality (OQ), thus providing a measure allowing the RCQ to be optimized by tuning the experimental setup. Additionally, the respective partial probability distributions can be obtained for the reactant and product states along the observed order parameter, even when these strongly overlap. The effects of both filtering (averaging) and uncorrelated noise are also examined. The approach is demonstrated on numerical examples and experimental single-molecule force probe data of the p5ab RNA hairpin and the apo-myoglobin protein at low pH, here focusing on the case of two-state kinetics

Maximizing information on the environment by dynamically controlled qubit probes

We explore the ability of a qubit probe to characterize unknown parameters of its environment. By resorting to quantum estimation theory, we analytically find the ultimate bound on the precision of estimating key parameters of a broad class of ubiquitous environmental noises ("baths") which the qubit may probe. These include the probe-bath coupling strength, the correlation time of generic bath spectra, the power laws governing these spectra, as well as their dephasing times T2. Our central result is that by optimizing the dynamical control on the probe under realistic constraints one may attain the maximal accuracy bound on the estimation of these parameters by the least number of measurements possible. Applications of this protocol that combines dynamical control and estimation theory tools to quantum sensing are illustrated for a nitrogen-vacancy center in diamond used as a probe.Comment: 8 pages + 6 pages (appendix), 3 Figure

Comment of Global dynamics of biological systems

In a recent study, (Grigorov, 2006) analyzed temporal gene expression profiles (Arbeitman et al., 2002) generated in a Drosophila experiment using SSA in conjunction with Monte-Carlo SSA. The author (Grigorov, 2006) makes three important claims in his article, namely: Claim1: A new method based on the theory of nonlinear time series analysis is used to capture the global dynamics of the fruit-fly cycle temporal gene expression profiles. Claim 2: Flattening of a significant part of the eigen-spectrum confirms the hypothesis about an underly-ing high-dimensional chaotic generating process. Claim 3: Monte-Carlo SSA can be used to establish whether a given time series is distinguishable from any well-defined process including deterministic chaos. In this report we present fundamental concerns with respect to the above claims (Grigorov, 2006) in a systematic manner with simple examples. The discussion provided especially discourages the choice of SSA for inferring nonlinear dynamical structure form time series obtained in any biological paradigm.Comment: 6 pages, 2 figure

Estimation of Power System Inertia Using Nonlinear Koopman Modes

We report a new approach to estimating power system inertia directly from time-series data on power system dynamics. The approach is based on the so-called Koopman Mode Decomposition (KMD) of such dynamic data, which is a nonlinear generalization of linear modal decomposition through spectral analysis of the Koopman operator for nonlinear dynamical systems. The KMD-based approach is thus applicable to dynamic data that evolve in nonlinear regime of power system characteristics. Its effectiveness is numerically evaluated with transient stability simulations of the IEEE New England test system.Comment: 10 pages, 4 figures, conferenc

Noise-robust quantum sensing via optimal multi-probe spectroscopy

The dynamics of quantum systems are unavoidably influenced by their environment and in turn observing a quantum system (probe) can allow one to measure its environment: Measurements and controlled manipulation of the probe such as dynamical decoupling sequences as an extension of the Ramsey interference measurement allow to spectrally resolve a noise field coupled to the probe. Here, we introduce fast and robust estimation strategies for the characterization of the spectral properties of classical and quantum dephasing environments. These strategies are based on filter function orthogonalization, optimal control filters maximizing the relevant Fisher Information and multi-qubit entanglement. We investigate and quantify the robustness of the schemes under different types of noise such as finite-precision measurements, dephasing of the probe, spectral leakage and slow temporal fluctuations of the spectrum.Comment: 13 pages, 14 figure