Estimation and uncertainty of reversible Markov models

Reversibility is a key concept in Markov models and Master-equation models of molecular kinetics. The analysis and interpretation of the transition matrix encoding the kinetic properties of the model relies heavily on the reversibility property. The estimation of a reversible transition matrix from simulation data is therefore crucial to the successful application of the previously developed theory. In this work we discuss methods for the maximum likelihood estimation of transition matrices from finite simulation data and present a new algorithm for the estimation if reversibility with respect to a given stationary vector is desired. We also develop new methods for the Bayesian posterior inference of reversible transition matrices with and without given stationary vector taking into account the need for a suitable prior distribution preserving the meta- stable features of the observed process during posterior inference. All algorithms here are implemented in the PyEMMA software - http://pyemma.org - as of version 2.0

Active phase and amplitude fluctuations of flagellar beating

The eukaryotic flagellum beats periodically, driven by the oscillatory dynamics of molecular motors, to propel cells and pump fluids. Small, but perceivable fluctuations in the beat of individual flagella have physiological implications for synchronization in collections of flagella as well as for hydrodynamic interactions between flagellated swimmers. Here, we characterize phase and amplitude fluctuations of flagellar bending waves using shape mode analysis and limit cycle reconstruction. We report a quality factor of flagellar oscillations, $Q=38.0\pm 16.7$ (mean$\pm$s.e.). Our analysis shows that flagellar fluctuations are dominantly of active origin. Using a minimal model of collective motor oscillations, we demonstrate how the stochastic dynamics of individual motors can give rise to active small-number fluctuations in motor-cytoskeleton systems.Comment: accepted for publication in Physical Review Letter

Chandra and Hubble Study of a New Transient X-ray Source in M31

We present X-ray and optical observations of a new transient X-ray source in M31 first detected 23-May-2004 at R.A.=00:43:09.940 +/- 0.65'', Dec.=41:23:32.49 +/- 0.66''. The X-ray lightcurve shows two peaks separated by several months, reminiscent of many Galactic X-ray novae. The location and X-ray spectrum of the source suggest it is a low mass X-ray binary (LMXB). Follow-up HST ACS observations of the location both during and after the outburst provide a high-confidence detection of variability for one star within the X-ray position error ellipse. This star has $\Delta$B ~ 1 mag, and there is only a ~1% chance of finding such a variable in the error ellipse. We consider this star a good candidate for the optical counterpart of the X-ray source. The luminosity of this candidate provides a prediction for the orbital period of the system of 2.3$^{+3.7}_{-1.2}$ days.Comment: 17 pages, 3 figures, 4 tables, accepted for publication in Ap

A Deep XMM-Newton Survey of M33: Point Source Catalog, Source Detection and Characterization of Overlapping Fields

We have obtained a deep 8-field XMM-Newton mosaic of M33 covering the galaxy out to the D$_{25}$ isophote and beyond to a limiting 0.2--4.5 keV unabsorbed flux of 5$\times$10$^{-16}$ erg cm$^{-2}$ s$^{-1}$ (L${>}$4$\times$10$^{34}$ erg s$^{-1}$ at the distance of M33). These data allow complete coverage of the galaxy with high sensitivity to soft sources such as diffuse hot gas and supernova remnants. Here we describe the methods we used to identify and characterize 1296 point sources in the 8 fields. We compare our resulting source catalog to the literature, note variable sources, construct hardness ratios, classify soft sources, analyze the source density profile, and measure the X-ray luminosity function. As a result of the large effective area of XMM-Newton below 1 keV, the survey contains many new soft X-ray sources. The radial source density profile and X-ray luminosity function for the sources suggests that only $\sim$15% of the 391 bright sources with L${>}$3.6$\times$10$^{35}$ erg s$^{-1}$ are likely to be associated with M33, and more than a third of these are known supernova remnants. The log(N)--log(S) distribution, when corrected for background contamination, is a relatively flat power-law with a differential index of 1.5, which suggests many of the other M33 sources may be high-mass X-ray binaries. Finally, we note the discovery of an interesting new transient X-ray source, which we are unable to classify.Comment: 26 pages, 6 tables, 13 figures, accepted for publication in ApJ

SXP214, an X-ray Pulsar in the Small Magellanic Cloud, Crossing the Circumstellar Disk of the Companion

Located in the Small Magellanic Cloud (SMC), SXP214 is an X-ray pulsar in a high mass X-ray binary system with a Be-star companion. A recent survey of the SMC under a Chandra X-ray Visionary program found the source in a transition when the X-ray flux was on a steady rise. The Lomb-Scargle periodogram revealed a pulse period of 211.49 +/- 0.42 s, which is significantly (>5sigma) shorter than the previous measurements with XMM-Newton and RXTE. This implies that the system has gone through sudden spin-up episodes recently. The pulse profile shows a sharp eclipse-like feature with a modulation amplitude of >95%. The linear rise of the observed X-ray luminosity from <~2x to 7x10^35 erg s^-1 is correlated with steady softening of the X-ray spectrum, which can be described by the changes in the local absorption from N_H ~ 10^24 to <~10^20 cm^-2 for an absorbed power-law model. The soft X-ray emission below 2 keV was absent in the early part of the observation when only the pulsating hard X-ray component was observed, whereas at later times both soft and hard X-ray components were observed pulsating. A likely explanation is that the neutron star was initially hidden in the circumstellar disk of the companion, and later came out of the disk with the accreted material that continued fueling the observed pulsation.Comment: 8 pages, 4 figures, 1 table, accepted for publication in Ap

Optical Constraints on an X-ray Transient Source in M31

We have detected a transient X-ray source in the M31 bulge through a continuing monitoring campaign with the Chandra ACIS-I camera. The source was detected at R.A.=00:42:33.428 +/- 0.11'', Dec.=+41:17:03.37 +/- 0.11'' in only a single observation taken 2004 May 23. Fortuitous optical HST/ACS imaging of the transient location prior to the X-ray outburst, along with follow-up HST/ACS imaging during and after the outburst, reveals no transient optical source brighter than B (equivalent) = 25.5. The location of the source and its X-ray properties suggest it is a low mass X-ray binary (LMXB). Assuming the transient is similar to many Galactic X-ray novae, the X-ray luminosity of (3.9 +/- 0.5) X 10$^{37}$ erg s$^{-1}$ and the upper-limit on the optical luminosity provide a prediction of <1.6 days for the orbital period of the binary system.Comment: 15 pages, 3 figures, accepted for publication in Ap

A Soft X-ray Transient in the M31 Bulge

We have examined a probable soft X-ray transient source in the M31 bulge at R.A.=0:42:41.814 +/- 0.08", Dec. = 41:16:35.86 +/- 0.07". On the three occasions we observed the source, its spectrum was soft (kT_{in} ~1 keV). The brightest detection of the source was 2004 July 17 with a 0.3-7 keV luminosity of ~5 X 10^{37} erg/s. The only previous detection of the source was in 1979 by the Einstein observatory. The multiple detections over 25 years suggest the duty cycle of the source is in the range 0.02-0.06. Coordinated HST/ACS imaging before, during, and after the outburst revealed no variable optical source within the position errors of the X-ray source. The optical data place a firm upper limit on the brightness of the counterpart of the X-ray outburst of B>24.7, suggesting the binary has a period <5.2 days. The X-ray spectrum and lack of bright stars at the source location indicate the source was a soft transient event occurring in a low-mass X-ray binary, making this source a good black hole candidate in M31.Comment: 18 pages, 4 tables, 3 figures, accepted for publication in Ap