Are biological systems poised at criticality?

Many of life's most fascinating phenomena emerge from interactions among many elements--many amino acids determine the structure of a single protein, many genes determine the fate of a cell, many neurons are involved in shaping our thoughts and memories. Physicists have long hoped that these collective behaviors could be described using the ideas and methods of statistical mechanics. In the past few years, new, larger scale experiments have made it possible to construct statistical mechanics models of biological systems directly from real data. We review the surprising successes of this "inverse" approach, using examples form families of proteins, networks of neurons, and flocks of birds. Remarkably, in all these cases the models that emerge from the data are poised at a very special point in their parameter space--a critical point. This suggests there may be some deeper theoretical principle behind the behavior of these diverse systems.Comment: 21 page

Highly-parallelized simulation of a pixelated LArTPC on a GPU

The rapid development of general-purpose computing on graphics processing units (GPGPU) is allowing the implementation of highly-parallelized Monte Carlo simulation chains for particle physics experiments. This technique is particularly suitable for the simulation of a pixelated charge readout for time projection chambers, given the large number of channels that this technology employs. Here we present the first implementation of a full microphysical simulator of a liquid argon time projection chamber (LArTPC) equipped with light readout and pixelated charge readout, developed for the DUNE Near Detector. The software is implemented with an end-to-end set of GPU-optimized algorithms. The algorithms have been written in Python and translated into CUDA kernels using Numba, a just-in-time compiler for a subset of Python and NumPy instructions. The GPU implementation achieves a speed up of four orders of magnitude compared with the equivalent CPU version. The simulation of the current induced on 10^3 pixels takes around 1 ms on the GPU, compared with approximately 10 s on the CPU. The results of the simulation are compared against data from a pixel-readout LArTPC prototype

Extracting Meaningful Slopes from Terrain Contours

Good quality terrain models are becoming more and more important, as applications such as runoff modelling are being developed that demand better surface orientation information than is available from traditional interpolation techniques. A consequence is that poor-quality elevation grids must be massaged before they provide useable runoff models. Rather than using direct data acquisition, this project concentrated on using available contour data because, despite modern techniques, contour maps are still the most available form of elevation information. Recent work on the automatic reconstruction of curves from point samples, and the generation of medial axis transforms (skeletons) has greatly helped in expressing the spatial relationships between topographic sets of contours. With these techniques the insertion of skeleton points into a TIN model guarantees the elimination of all "flat triangles" where all three vertices have the same elevation. Additional assumptions about the local uniformity of slopes give us enough information to assign elevation values to these skeleton points. In addition, various interpolation techniques were compared using the enriched contour data. Examination of the quality and consistency of the resulting maps indicates the required properties of the interpolation method in order to produce terrain models with valid slopes. The result provides us with a surprisingly realistic model of the surface - that is, one that conforms well to our subjective interpretation of what a real landscape should look like

Asynchronously Communicating Visibly Pushdown Systems

Abstract. We introduce an automata-based formal model suitable for specifying, modeling, analyzing, and verifying asynchronous task-based and message-passing programs. Our model consists of visibly pushdown automata communicating over unbounded reliable point-to-point firstin-first-out queues. Such a combination unifies two branches of research, one focused on task-based models, and the other on models of messagepassing programs. Our model generalizes previously proposed models that have decidable reachability in several ways. Unlike task-based models of asynchronous programs, our model allows sending and receiving of messages even when stacks are not empty, without imposing restrictions on the number of context-switches or communication topology. Our model also generalizes the well-known communicating finite-state machines with recognizable channel property allowing (1) individual components to be visibly pushdown automata, which are more suitable for modeling (possibly recursive) programs, (2) the set of words (i.e., languages) of messages on queues to form a visibly pushdown language, which permits modeling of remote procedure calls and simple forms of counting, and (3) the relations formed by tuples of such languages to be synchronized, which permits modeling of complex interactions among processes. In spite of these generalizations, we prove that the composite configuration and control-state reachability are still decidable for our model.

The cost-utility of magnetic resonance imaging for breast cancer in BRCA1 mutation carriers aged 30–49

BRCA1, MRI, Mammography, Surveillance, Cost-utility,