Characterizing and tracking single colloidal particles with video holographic microscopy

We use digital holographic microscopy and Mie scattering theory to simultaneously characterize and track individual colloidal particles. Each holographic snapshot provides enough information to measure a colloidal sphere's radius and refractive index to within 1%, and simultaneously to measure its three-dimensional position with nanometer in-plane precision and 10 nanometer axial resolution.Comment: 6 pages, 3 figure

Parallel Search with no Coordination

We consider a parallel version of a classical Bayesian search problem. $k$ agents are looking for a treasure that is placed in one of the boxes indexed by $\mathbb{N}^+$ according to a known distribution $p$. The aim is to minimize the expected time until the first agent finds it. Searchers run in parallel where at each time step each searcher can "peek" into a box. A basic family of algorithms which are inherently robust is \emph{non-coordinating} algorithms. Such algorithms act independently at each searcher, differing only by their probabilistic choices. We are interested in the price incurred by employing such algorithms when compared with the case of full coordination. We first show that there exists a non-coordination algorithm, that knowing only the relative likelihood of boxes according to $p$, has expected running time of at most $10+4(1+\frac{1}{k})^2 T$, where $T$ is the expected running time of the best fully coordinated algorithm. This result is obtained by applying a refined version of the main algorithm suggested by Fraigniaud, Korman and Rodeh in STOC'16, which was designed for the context of linear parallel search.We then describe an optimal non-coordinating algorithm for the case where the distribution $p$ is known. The running time of this algorithm is difficult to analyse in general, but we calculate it for several examples. In the case where $p$ is uniform over a finite set of boxes, then the algorithm just checks boxes uniformly at random among all non-checked boxes and is essentially $2$ times worse than the coordinating algorithm.We also show simple algorithms for Pareto distributions over $M$ boxes. That is, in the case where $p(x) \sim 1/x^b$ for $0< b < 1$, we suggest the following algorithm: at step $t$ choose uniformly from the boxes unchecked in ${1, . . . ,min(M, \lfloor t/\sigma\rfloor)}$, where $\sigma = b/(b + k - 1)$. It turns out this algorithm is asymptotically optimal, and runs about $2+b$ times worse than the case of full coordination

Analysis of the Brinkman-Forchheimer equations with slip boundary conditions

In this work, we study the Brinkman-Forchheimer equations driven under slip boundary conditions of friction type. We prove the existence and uniqueness of weak solutions by means of regularization combined with the Faedo-Galerkin approach. Next we discuss the continuity of the solution with respect to Brinkman's and Forchheimer's coefficients. Finally, we show that the weak solution of the corresponding stationary problem is stable

Demographic buffering and compensatory recruitment promotes the persistence of disease in a wildlife population.

Published onlineLETTERDemographic buffering allows populations to persist by compensating for fluctuations in vital rates, including disease-induced mortality. Using long-term data on a badger (Meles meles Linnaeus, 1758) population naturally infected with Mycobacterium bovis, we built an integrated population model to quantify impacts of disease, density and environmental drivers on survival and recruitment. Badgers exhibit a slow life-history strategy, having high rates of adult survival with low variance, and low but variable rates of recruitment. Recruitment exhibited strong negative density-dependence, but was not influenced by disease, while adult survival was density independent but declined with increasing prevalence of diseased individuals. Given that reproductive success is not depressed by disease prevalence, density-dependent recruitment of cubs is likely to compensate for disease-induced mortality. This combination of slow life history and compensatory recruitment promotes the persistence of a naturally infected badger population and helps to explain the badger's role as a persistent reservoir of M. bovis.NERCUK Department of Environment, Food and Rural Affair

CRANKITE: a fast polypeptide backbone conformation sampler

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details. Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space. Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length

Perceptual Context in Cognitive Hierarchies

Cognition does not only depend on bottom-up sensor feature abstraction, but also relies on contextual information being passed top-down. Context is higher level information that helps to predict belief states at lower levels. The main contribution of this paper is to provide a formalisation of perceptual context and its integration into a new process model for cognitive hierarchies. Several simple instantiations of a cognitive hierarchy are used to illustrate the role of context. Notably, we demonstrate the use context in a novel approach to visually track the pose of rigid objects with just a 2D camera

Cryotomography of budding influenza a virus reveals filaments with diverse morphologies that mostly do not bear a genome at their distal end

Influenza viruses exhibit striking variations in particle morphology between strains. Clinical isolates of influenza A virus have been shown to produce long filamentous particles while laboratory-adapted strains are predominantly spherical. However, the role of the filamentous phenotype in the influenza virus infectious cycle remains undetermined. We used cryo-electron tomography to conduct the first three-dimensional study of filamentous virus ultrastructure in particles budding from infected cells. Filaments were often longer than 10 microns and sometimes had bulbous heads at their leading ends, some of which contained tubules we attribute to M1 while none had recognisable ribonucleoprotein (RNP) and hence genome segments. Long filaments that did not have bulbs were infrequently seen to bear an ordered complement of RNPs at their distal ends. Imaging of purified virus also revealed diverse filament morphologies; short rods (bacilliform virions) and longer filaments. Bacilliform virions contained an ordered complement of RNPs while longer filamentous particles were narrower and mostly appeared to lack this feature, but often contained fibrillar material along their entire length. The important ultrastructural differences between these diverse classes of particles raise the possibility of distinct morphogenetic pathways and functions during the infectious process

The impact of ocean acidification on the functional morphology of foraminifera

This work was supported by the NERC UK Ocean Acidification Research Programme grant NE/H017445/1. WENA acknowledges NERC support (NE/G018502/1). DMP received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions.Culturing experiments were performed on sediment samples from the Ythan Estuary, N. E. Scotland, to assess the impacts of ocean acidification on test surface ornamentation in the benthic foraminifer Haynesina germanica. Specimens were cultured for 36 weeks at either 380, 750 or 1000 ppm atmospheric CO2. Analysis of the test surface using SEM imaging reveals sensitivity of functionally important ornamentation associated with feeding to changing seawater CO2 levels. Specimens incubated at high CO2 levels displayed evidence of shell dissolution, a significant reduction and deformation of ornamentation. It is clear that these calcifying organisms are likely to be vulnerable to ocean acidification. A reduction in functionally important ornamentation could lead to a reduction in feeding efficiency with consequent impacts on this organism’s survival and fitness.Publisher PDFPeer reviewe

Dynamic Limits on Planar Libration-Orbit Coupling Around an Oblate Primary

This paper explores the dynamic properties of the planar system of an ellipsoidal satellite in an equatorial orbit about an oblate primary. In particular, we investigate the conditions for which the satellite is bound in librational motion or when the satellite will circulate with respect to the primary. We find the existence of stable equilibrium points about which the satellite can librate, and explore both the linearized and non-linear dynamics around these points. Absolute bounds are placed on the phase space of the libration-orbit coupling through the use of zero-velocity curves that exist in the system. These zero-velocity curves are used to derive a sufficient condition for when the satellite's libration is bound to less than 90 degrees. When this condition is not satisfied so that circulation of the satellite is possible, the initial conditions at zero libration angle are determined which lead to circulation of the satellite. Exact analytical conditions for circulation and the maximum libration angle are derived for the case of a small satellite in orbits of any eccentricity.Comment: Submitted to Celestial Mechanics and Dynamical Astronom