Ten Quick Tips for Using a Raspberry Pi

Much of biology (and, indeed, all of science) is becoming increasingly computational. We tend to think of this in regards to algorithmic approaches and software tools, as well as increased computing power. There has also been a shift towards slicker, packaged solutions--which mirrors everyday life, from smart phones to smart homes. As a result, it's all too easy to be detached from the fundamental elements that power these changes, and to see solutions as "black boxes". The major goal of this piece is to use the example of the Raspberry Pi--a small, general-purpose computer--as the central component in a highly developed ecosystem that brings together elements like external hardware, sensors and controllers, state-of-the-art programming practices, and basic electronics and physics, all in an approachable and useful way. External devices and inputs are easily connected to the Pi, and it can, in turn, control attached devices very simply. So whether you want to use it to manage laboratory equipment, sample the environment, teach bioinformatics, control your home security or make a model lunar lander, it's all built from the same basic principles. To quote Richard Feynman, "What I cannot create, I do not understand".Comment: 12 pages, 2 figure

Investigation about crack propagation paths in thin rim gears

Crack propagation in gears is a problem related not only to the life of the components, but also to the concept of failsafe design. Fail safe design means to design a component in order that, if a failure occurs, this may cause a "safe failure". This aspect is very important above all in aerospace industry. As a matter of fact, in aerospace application, the need of reducing weight brings to produce gears with very thick rim and web. Considering thin rim gears, when a crack is nucleated near the tooth root, it may propagate through the tooth (causing the loss of the entire tooth or a portion of it) or the propagation may follow a path across the wheel diameter (causing the projection of big parts of the gear that may break the gearbox and may cause serious damage to the aircraft). The first failure mode is define as "failsafe failure" and the second one as "catastrophic failure" and of course has to be avoided. Designers need to have robust design criteria in order to predict crack propagation paths and to avoid catastrophic failures. In literature, few works are present concerning this topic, in particular related to the effect of geometrical parameters that may affect the crack propagation. In this work a numerical analysis about crack propagation in gears with respect to the backup ratio (ratio between tooth height and rim thickness), initial crack position and shape has been done by means of the Extended FEM (XFEM) technique, realizing 3D models. XFEM 3D is a relatively new technique consisting in enriching traditional finite elements with more complex shape functions; in this way it is possible to propagate crack also between mesh nodes and to have mesh independent results. Aim of this paper is to highlight the crack propagation path in order to give to designers an high confident design criterion, related to the gear geometry. In particular, the effect of both rim thickness and orientation of the initial crack have been considered in order to enrich the literature knowledge. Numerical results obtained in this work have been compared with those found in the literature, showing a very good correlation

An atomic mechanism for the boson peak in metallic glasses

The boson peak in metallic glasses is modeled in terms of local structural shear rearrangements. Using Eshelby's solution of the corresponding elasticity theory problem (J. D. Eshelby, Proc. Roy. Soc. A241, 376 (1957)), one can calculate the saddle point energy of such a structural rearrangement. The neighbourhood of the saddle point gives rise to soft resonant vibrational modes. One can calculate their density, their kinetic energy, their fourth order potential term and their coupling to longitudinal and transverse sound waves.Comment: 9 pages, 7 figures, 31 references, contribution to 11th International Workshop on Complex Systems, Andalo (Italy), March 200

Point defect in solids: Shear dominance of the far-field energy

It is shown that the elastic energy far from a point defect in an isotropic solid is mainly shear elastic energy. The calculation, which is based on a standard dipole expansion, shows that no matter how large or small the bulk modulus is compared to the shear modulus, less than 10% of the distant point defect energy is associated with volume changes.Comment: Brief not

The intrinsic Baldwin effect in broad Balmer lines of six long-term monitored AGNs

We investigate the intrinsic Baldwin effect (Beff) of the broad H$\alpha$ and H$\beta$ emission lines for six Type 1 active galactic nuclei (AGNs) with different broad line characteristics: two Seyfert 1 (NGC 4151 and NGC 5548), two AGNs with double-peaked broad line profiles (3C 390.3 and Arp 102B), one narrow line Seyfert 1 (Ark 564), and one high-luminosity quasar with highly red asymmetric broad line profiles (E1821+643). We found that a significant intrinsic Beff was present in all Type 1 AGNs in our sample. Moreover, we do not see strong difference in intrinsic Beff slopes in different types of AGNs which probably have different physical properties, such as inclination, broad line region geometry, or accretion rate. Additionally, we found that the intrinsic Beff was not connected with the global one, which, instead, could not be detected in the broad H$\alpha$ or H$\beta$ emission lines. In the case of NGC 4151, the detected variation of the Beff slope could be due to the change in the site of line formation in the BLR. Finally, the intrinsic Beff might be caused by the additional optical continuum component that is not part of the ionization continuum.Comment: 12 pages, 8 figures, Accepted for publication in A&

Beyond the fundamental noise limit in coherent optical fiber links

It is well known that temperature variations and acoustic noise affect ultrastable frequency dissemination along optical fiber. Active stabilization techniques are in general adopted to compensate for the fiber-induced phase noise. However, despite this compensation, the ultimate link performances remain limited by the so called delay-unsuppressed fiber noise that is related to the propagation delay of the light in the fiber. In this paper, we demonstrate a data post-processing approach which enables us to overcome this limit. We implement a subtraction algorithm between the optical signal delivered at the remote link end and the round-trip signal. In this way, a 6 dB improvement beyond the fundamental limit imposed by delay-unsuppressed noise is obtained. This result enhances the resolution of possible comparisons between remote optical clocks by a factor of 2. We confirm the theoretical prediction with experimental data obtained on a 47 km metropolitan fiber link, and propose how to extend this method for frequency dissemination purposes as well

Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis

BACKGROUND: Bacterial spores are important contaminants in food, and the spore forming bacteria are often implicated in food safety and food quality considerations. Spore formation is a complex developmental process involving the expression of more than 500 genes over the course of 6 to 8 hrs. The process culminates in the formation of resting cells capable of resisting environmental extremes and remaining dormant for long periods of time, germinating when conditions promote further vegetative growth. Experimental observations of sporulation and germination are problematic and time consuming so that reliable models are an invaluable asset in terms of prediction and risk assessment. In this report we develop a model which assists in the interpretation of sporulation dynamics. RESULTS: This paper defines and analyses a mathematical model for the network regulating Bacillus subtilis sporulation initiation, from sensing of sporulation signals down to the activation of the early genes under control of the master regulator Spo0A. Our model summarises and extends other published modelling studies, by allowing the user to execute sporulation initiation in a scenario where Isopropyl β-D-1-thiogalactopyranoside (IPTG) is used as an artificial sporulation initiator as well as in modelling the induction of sporulation in wild-type cells. The analysis of the model results and the comparison with experimental data indicate that the model is good at predicting inducible responses to sporulation signals. However, the model is unable to reproduce experimentally observed accumulation of phosphorelay sporulation proteins in wild type B. subtilis. This model also highlights that the phosphorelay sub-component, which relays the signals detected by the sensor kinases to the master regulator Spo0A, is crucial in determining the response dynamics of the system. CONCLUSION: We show that there is a complex connectivity between the phosphorelay features and the master regulatory Spo0A. Additional we discovered that the experimentally observed regulation of the phosphotransferase Spo0B for wild-type B. subtilis may be playing an important role in the network which suggests that modelling of sporulation initiation may require additional experimental support. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12918-014-0119-x) contains supplementary material, which is available to authorized users

Walk2Map: Extracting Floor Plans from Indoor Walk Trajectories

Recent years have seen a proliferation of new digital products for the efficient management of indoor spaces, with important applications like emergency management, virtual property showcasing and interior design. While highly innovative and effective, these products rely on accurate 3D models of the environments considered, including information on both architectural and non-permanent elements. These models must be created from measured data such as RGB-D images or 3D point clouds, whose capture and consolidation involves lengthy data workflows. This strongly limits the rate at which 3D models can be produced, preventing the adoption of many digital services for indoor space management. We provide a radical alternative to such data-intensive procedures by presenting Walk2Map, a data-driven approach to generate floor plans only from trajectories of a person walking inside the rooms. Thanks to recent advances in data-driven inertial odometry, such minimalistic input data can be acquired from the IMU readings of consumer-level smartphones, which allows for an effortless and scalable mapping of real-world indoor spaces. Our work is based on learning the latent relation between an indoor walk trajectory and the information represented in a floor plan: interior space footprint, portals, and furniture. We distinguish between recovering area-related (interior footprint, furniture) and wall-related (doors) information and use two different neural architectures for the two tasks: an image-based Encoder-Decoder and a Graph Convolutional Network, respectively. We train our networks using scanned 3D indoor models and apply them in a cascaded fashion on an indoor walk trajectory at inference time. We perform a qualitative and quantitative evaluation using both trajectories simulated from scanned models of interiors and measured, real-world trajectories, and compare against a baseline method for image-to-image translation. The experiments confirm that our technique is viable and allows recovering reliable floor plans from minimal walk trajectory data