The Perception of Globally Coherent Motion

How do human observers perceive a coherent pattern of motion from a disparate set of local motion measures? Our research has examined how ambiguous motion signals along straight contours are spatially integrated to obtain a globally coherent perception of motion. Observers viewed displays containing a large number of apertures, with each aperture containing one or more contours whose orientations and velocities could be independently specified. The total pattern of the contour trajectories across the individual apertures was manipulated to produce globally coherent motions, such as rotations, expansions, or translations. For displays containing only straight contours extending to the circumferences of the apertures, observers' reports of global motion direction were biased whenever the sampling of contour orientations was asymmetric relative to the direction of motion. Performance was improved by the presence of identifiable features, such as line ends or crossings, whose trajectories could be tracked over time. The reports of our observers were consistent with a pooling process involving a vector average of measures of the component of velocity normal to contour orientation, rather than with the predictions of the intersection-of-constraints analysis in velocity space.Air Force Office of Scientific Research (90-0175, 89-0016); National Science Foundation, Office of Naval Research, Air Force Office of Scientific Research (BNS-8908426

Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters

The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our analysis reveals that the proximity of the tethered bead to a nearby surface (the microscope slide) gives rise to a volume-exclusion effect, resulting in an entropic force on the molecule. This force stretches the molecule, changing its statistical properties. In particular, the proximity of bead and surface brings about intriguing scaling relations between key observables (statistical moments of the bead) and parameters such as the bead size and contour length of the molecule. We present both approximate analytic solutions and numerical results for these effects in both flexible and semiflexible tethers. Finally, our results give a precise, experimentally-testable prediction for the probability distribution of the distance between the polymer attachment point and the center of the mobile bead.Comment: 4 pages, 3 figure

The Collimated Jet Source in IRAS 16547-4247: Time Variation, Possible Precession, and Upper Limits to the Proper Motions Along the Jet Axis

The triple radio source detected in association with the luminous infrared source IRAS 16547-4247 has previously been studied with high angular resolution and high sensitivity with the Very Large Array (VLA) at 3.6-cm wavelength. In this paper, we present new 3.6 cm observations taken 2.68 years after the first epoch that allow a search for variability and proper motions, as well as the detection of additional faint sources in the region. We do not detect proper motions along the axis of the outflow in the outer lobes of this source at a 4-$\sigma$ upper limit of $\sim$160 km s$^{-1}$. This suggests that these lobes are probably working surfaces where the jet is interacting with a denser medium. However, the brightest components of the lobes show evidence of precession, at a rate of $0\rlap.^\circ08$ yr$^{-1}$ clockwise in the plane of the sky. It may be possible to understand the distribution of almost all the identified sources as the result of ejecta from a precessing jet. The core of the thermal jet shows significant variations in flux density and morphology. We compare this source with other jets in low and high mass young stars and suggest that the former can be understood as a scaled-up version of the latter.Comment: 26 pages, 9 figure

Conformational Dynamics of Supramolecular Protein Assemblies in the EMDB

The Electron Microscopy Data Bank (EMDB) is a rapidly growing repository for the dissemination of structural data from single-particle reconstructions of supramolecular protein assemblies including motors, chaperones, cytoskeletal assemblies, and viral capsids. While the static structure of these assemblies provides essential insight into their biological function, their conformational dynamics and mechanics provide additional important information regarding the mechanism of their biological function. Here, we present an unsupervised computational framework to analyze and store for public access the conformational dynamics of supramolecular protein assemblies deposited in the EMDB. Conformational dynamics are analyzed using normal mode analysis in the finite element framework, which is used to compute equilibrium thermal fluctuations, cross-correlations in molecular motions, and strain energy distributions for 452 of the 681 entries stored in the EMDB at present. Results for the viral capsid of hepatitis B, ribosome-bound termination factor RF2, and GroEL are presented in detail and validated with all-atom based models. The conformational dynamics of protein assemblies in the EMDB may be useful in the interpretation of their biological function, as well as in the classification and refinement of EM-based structures.Comment: Associated online data bank available at: http://lcbb.mit.edu/~em-nmdb

Analysis of a Fragmenting Sunspot using Hinode Observations

We employ high resolution filtergrams and polarimetric measurements from Hinode to follow the evolution of a sunspot for eight days starting on June 28, 2007. The imaging data were corrected for intensity gradients, projection effects, and instrumental stray light prior to the analysis. The observations show the formation of a light bridge at one corner of the sunspot by a slow intrusion of neighbouring penumbral filaments. This divided the umbra into two individual umbral cores. During the light bridge formation, there was a steep increase in its intensity from 0.28 to 0.7 I_QS in nearly 4 hr, followed by a gradual increase to quiet Sun (QS) values in 13 hr. This increase in intensity was accompanied by a large reduction in the field strength from 1800 G to 300 G. The smaller umbral core gradually broke away from the parent sunspot nearly 2 days after the formation of the light bridge rendering the parent spot without a penumbra at the location of fragmentation. The penumbra in the fragment disappeared first within 34 hr, followed by the fragment whose area decayed exponentially with a time constant of 22 hr. The depleted penumbra in the parent sunspot regenerated when the inclination of the magnetic field at the penumbra-QS boundary became within 40 deg. from being completely horizontal and this occurred near the end of the fragment's lifetime. After the disappearance of the fragment, another light bridge formed in the parent which had similar properties as the fragmenting one, but did not divide the sunspot. The significant weakening in field strength in the light bridge along with the presence of granulation is suggestive of strong convection in the sunspot which might have triggered the expulsion and fragmentation of the smaller spot. Although the presence of QS photospheric conditions in sunspot umbrae could be a necessary condition for fragmentation, it is not a sufficient one.Comment: Accepted for publication in ApJ; 15 pages, 15 figures, 1 tabl