The Glass Transition and the Jarzynski Equality

A simple model featuring a double well potential is used to represent a liquid that is quenched from an ergodic state into a history dependent glassy state. Issues surrounding the application of the Jarzynski Equality to glass formation are investigated. We demonstrate that the Jarzynski Equality gives the free energy difference between the initial state and the state we would obtain if the glass relaxed to true thermodynamic equilibrium. We derive new variations of the Jarzynski Equality which are relevant to the history dependent glassy state rather than the underlying equilibrium state. It is shown how to compute the free energy differences for the nonequilibrium history dependent glassy state such that it remains consistent with the standard expression for the entropy and with the second law inequality.Comment: 16 pages, 5 figure

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

FALCON: a software package for analysis of nestedness in bipartite networks

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.Nestedness is a statistical measure used to interpret bipartite interaction data in several ecological and evolutionary contexts, e.g. biogeography (species-site relationships) and species interactions (plant-pollinator and host-parasite networks). Multiple methods have been used to evaluate nestedness, which differ in how the metrics for nestedness are determined. Furthermore, several different null models have been used to calculate statistical significance of nestedness scores. The profusion of measures and null models, many of which give conflicting results, is problematic for comparison of nestedness across different studies. We developed the FALCON software package to allow easy and efficient comparison of nestedness scores and statistical significances for a given input network, using a selection of the more popular measures and null models from the current literature. FALCON currently includes six measures and five null models for nestedness in binary networks, and two measures and four null models for nestedness in weighted networks. The FALCON software is designed to be efficient and easy to use. FALCON code is offered in three languages (R, MATLAB, Octave) and is designed to be modular and extensible, enabling users to easily expand its functionality by adding further measures and null models. FALCON provides a robust methodology for comparing the strength and significance of nestedness in a given bipartite network using multiple measures and null models. It includes an “adaptive ensemble” method to reduce undersampling of the null distribution when calculating statistical significance. It can work with binary or weighted input networks. FALCON is a response to the proliferation of different nestedness measures and associated null models in the literature. It allows easy and efficient calculation of nestedness scores and statistical significances using different methods, enabling comparison of results from different studies and thereby supporting theoretical study of the causes and implications of nestedness in different biological contexts

Avoiding unintentional eviction from integral projection models

Integral projection models (IPMs) are increasingly being applied to study size-structured populations. Here we call attention to a potential problem in their construction that can have important consequences for model results. IPMs are implemented using an approximating matrix and bounded size range. Individuals near the size limits can be unknowingly "evicted" from the model because their predicted future size is outside the range. We provide simple measures for the magnitude of eviction and the sensitivity of the population growth rate (lambda) to eviction, allowing modelers to assess the severity of the problem in their IPM. For IPMs of three plant species, we found that eviction occurred in all cases and caused underestimation of the population growth rate (lambda) relative to eviction-free models; it is likely that other models are similarly affected. Models with frequent eviction should be modified because eviction is only possible when size transitions are badly mis-specified. We offer several solutions to eviction problems, but we emphasize that the modeler must choose the most appropriate solution based on an understanding of why eviction occurs in the first place. We recommend testing IPMs for eviction problems and resolving them, so that population dynamics are modeled more accurately

Design and experimental characterization of a tunable vibration-based electromagnetic micro-generator

Vibration-based micro-generators, as an alternative source of energy, have become increasingly significant in the last decade. This paper presents a new tunable electromagnetic vibration-based micro-generator. Frequency tuning is realized by applying an axial tensile force to the micro-generator. The dimensions of the generator, especially the dimensions of the coil and the air gap between magnets, have been optimized to maximize the output voltage and power of the micro-generator. The resonant frequency has been successfully tuned from 67.6 to 98 Hz when various axial tensile forces were applied to the structure. The generator produced a power of 61.6–156.6 µW over the tuning range when excited at vibrations of 0.59 ms-2. The tuning mechanism has little effect on the total damping. When the tuning force applied on the generator becomes larger than the generator’s inertial force, the total damping increases resulting in reduced output power. The resonant frequency increases less than indicated from simulation and approaches that of a straight tensioned cable when the force associated with the tension in the beam becomes much greater than the beam stiffness. The test results agree with the theoretical analysis presented

Ontogeny and development of the tritocerebral commissure giant (TCG): an identified neuron in the brain of the grasshopper Schistocerca gregaria

The tritocerebral commissure giant (TCG) of the grasshopper Schistocerca gregaria is one of the best anatomically and physiologically described arthropod brain neurons. A member of the so-called Ventral Giant cluster of cells, it integrates sensory information from visual, antennal and hair receptors, and synapses with thoracic motor neurons in order to initiate and regulate flight behavior. Its ontogeny, however, remains unclear. In this study, we use bromodeoxyuridine incorporation and cyclin labeling to reveal proliferative neuroblasts in the region of the embryonic brain where the ventral giant cluster is located. Engrailed labeling confirms the deutocerebral identity of this cluster. Comparison of soma locations and initial neurite projections into tracts of the striate deutocerebrum help identify the cells of the ventral cluster in both the embryonic and adult brain. Reconstructions of embryonic cell lineages suggest deutocerebral NB1 as being the putative neuroblast of origin. Intracellular dye injection coupled with immunolabeling against neuron-specific horseradish peroxidase is used to identify the VG1 (TCG) and VG3 neurons from the ventral cluster in embryonic brain slices. Dye injection and backfilling are used to document axogenesis and the progressive expansion of the dendritic arbor of the TCG from mid-embryogenesis up to hatching. Comparative maps of embryonic neuroblasts from several orthopteroid insects suggest equivalent deutocerebral neuroblasts from which the homologous TCG neurons already identified in the adult brain could originate. Our data offer the prospect of identifying further lineage-related neurons from the cluster and so understand a brain connectome from both a developmental and evolutionary perspective