A Simple Kinetic Model Describes the Processivity of Myosin-V

Myosin-V is a motor protein responsible for organelle and vesicle transport in cells. Recent single-molecule experiments have shown that it is an efficient processive motor that walks along actin filaments taking steps of mean size close to 36 nm. A theoretical study of myosin-V motility is presented following an approach used successfully to analyze the dynamics of conventional kinesin but also taking some account of step-size variations. Much of the present experimental data for myosin-V can be well described by a two-state chemical kinetic model with three load-dependent rates. In addition, the analysis predicts the variation of the mean velocity and of the randomness -- a quantitative measure of the stochastic deviations from uniform, constant-speed motion -- with ATP concentration under both resisting and assisting loads, and indicates a {\it sub}step of size $d_{0} \simeq$ 13-14 nm (from the ATP-binding site) that appears to accord with independent observations.Comment: 20 pages, 7 figures, to be published in Biophys. J. in 200

Towards high-throughput 3D insect capture for species discovery and diagnostics

Digitisation of natural history collections not only preserves precious information about biological diversity, it also enables us to share, analyse, annotate and compare specimens to gain new insights. High-resolution, full-colour 3D capture of biological specimens yields color and geometry information complementary to other techniques (e.g., 2D capture, electron scanning and micro computed tomography). However 3D colour capture of small specimens is slow for reasons including specimen handling, the narrow depth of field of high magnification optics, and the large number of images required to resolve complex shapes of specimens. In this paper, we outline techniques to accelerate 3D image capture, including using a desktop robotic arm to automate the insect handling process; using a calibrated pan-tilt rig to avoid attaching calibration targets to specimens; using light field cameras to capture images at an extended depth of field in one shot; and using 3D Web and mixed reality tools to facilitate the annotation, distribution and visualisation of 3D digital models.Comment: 2 pages, 1 figure, for BigDig workshop at 2017 eScience conferenc

Microdissection of human chromosomes by a laser microbeam

A laser microbeam apparatus, based on an excimer laser pumped dye laser is used to microdissect human chromosomes and to isolate a single chromosome slice

'Colour and communion': Exploring the influences of visual art-making as a leisure activity on older women's subjective well-being

This is the post-print version of the final paper published in Journal of Aging Studies. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2009 Elsevier B.V.Research into the subjective experience of art-making for older people is limited, and has focused mostly on professional artists rather than amateurs. This study examined older women's motives for visual art-making. Thirty-two participants aged 60-86 years old were interviewed. Twelve lived with chronic illness; twenty reported good health. Nearly all had taken up art after retirement; two had since become professional artists. Participants described their art-making as enriching their mental life, promoting enjoyment of the sensuality of colour and texture, presenting new challenges, playful experimentation, and fresh ambitions. Art also afforded participants valued connections with the world outside the home and immediate family. It encouraged attention to the aesthetics of the physical environment, preserved equal status relationships, and created opportunities for validation. Art-making protected the women's identities, helping them to resist the stereotypes and exclusions which are commonly encountered in later life.AHR

A customisable pipeline for continuously harvesting socially-minded Twitter users

On social media platforms and Twitter in particular, specific classes of users such as influencers have been given satisfactory operational definitions in terms of network and content metrics. Others, for instance online activists, are not less important but their characterisation still requires experimenting. We make the hypothesis that such interesting users can be found within temporally and spatially localised contexts, i.e., small but topical fragments of the network containing interactions about social events or campaigns with a significant footprint on Twitter. To explore this hypothesis, we have designed a continuous user profile discovery pipeline that produces an ever-growing dataset of user profiles by harvesting and analysing contexts from the Twitter stream. The profiles dataset includes key network and content-based users metrics, enabling experimentation with user-defined score functions that characterise specific classes of online users. The paper describes the design and implementation of the pipeline and its empirical evaluation on a case study consisting of healthcare-related campaigns in the UK, showing how it supports the operational definitions of online activism, by comparing three experimental ranking functions. The code is publicly available.Comment: Procs. ICWE 2019, June 2019, Kore

Elastic lever arm model for myosin V

We present a mechanochemical model for myosin V, a two-headed processive motor protein. We derive the properties of a dimer from those of an individual head, which we model both with a 4-state cycle (detached, attached with ADP.Pi, attached with ADP and attached without nucleotide) and alternatively with a 5-state cycle (where the power stroke is not tightly coupled to the phosphate release). In each state the lever arm leaves the head at a different, but fixed, angle. The lever arm itself is described as an elastic rod. The chemical cycles of both heads are coordinated exclusively by the mechanical connection between the two lever arms. The model explains head coordination by showing that the lead head only binds to actin after the power stroke in the trail head and that it only undergoes its power stroke after the trail head unbinds from actin. Both models (4- and 5-state) reproduce the observed hand-over-hand motion and fit the measured force-velocity relations. The main difference between the two models concerns the load dependence of the run length, which is much weaker in the 5-state model. We show how systematic processivity measurement under varying conditions could be used to distinguish between both models and to determine the kinetic parameters.Comment: 15 pages, 15 figures, to appear in Biophys.

A Multiagent CyberBattleSim for RL Cyber Operation Agents

Hardening cyber physical assets is both crucial and labor-intensive. Recently, Machine Learning (ML) in general and Reinforcement Learning RL) more specifically has shown great promise to automate tasks that otherwise would require significant human insight/intelligence. The development of autonomous RL agents requires a suitable training environment that allows us to quickly evaluate various alternatives, in particular how to arrange training scenarios that pit attackers and defenders against each other. CyberBattleSim is a training environment that supports the training of red agents, i.e., attackers. We added the capability to train blue agents, i.e., defenders. The paper describes our changes and reports on the results we obtained when training blue agents, either in isolation or jointly with red agents. Our results show that training a blue agent does lead to stronger defenses against attacks. In particular, training a blue agent jointly with a red agent increases the blue agent's capability to thwart sophisticated red agents.Comment: To appear in Proceedings of the 2022 International Conference on Computational Science and Computational Intelligenc

Mass-varying neutrino in light of cosmic microwave background and weak lensing

We aim to constrain mass-varying neutrino models using large scale structure observations and produce forecast for the Euclid survey. We investigate two models with different scalar field potential and both positive and negative coupling parameters \beta. These parameters correspond to growing or decreasing neutrino mass, respectively. We explore couplings up to |\beta|<5. In the case of the exponential potential, we find an upper limit on $\Omega_\nu h^2$<0.004 at 2-$\sigma$ level. In the case of the inverse power law potential the null coupling can be excluded with more than 2-\sigma significance; the limits on the coupling are \beta>3 for the growing neutrino mass and \beta<-1.5 for the decreasing mass case. This is a clear sign for a preference of higher couplings. When including a prior on the present neutrino mass the upper limit on the coupling becomes |\beta|<3 at 2-$\sigma$ level for the exponential potential. Finally, we present a Fisher forecast using the tomographic weak lensing from an Euclid-like experiment and we also consider the combination with the cosmic microwave background (CMB) temperature and polarisation spectra from a Planck-like mission. If considered alone, lensing data is more efficient in constraining $\Omega_\nu$ with respect to CMB data alone. There is, however, a strong degeneracy in the \beta-$\Omega_\nu h^2$ plane. When the two data sets are combined, the latter degeneracy remains, but the errors are reduced by a factor ~2 for both parameters.Comment: 5 pages, 6 figures. Now published in A&A 500, 657-665 (2009

Quantum metastability in time-periodic potentials

In this paper we investigate quantum metastability of a particle trapped in between an infinite wall and a square barrier, with either a time-periodically oscillating barrier (Model A) or bottom of the well (Model B). Based on the Floquet theory, we derive in each case an equation which determines the stability of the metastable system. We study the influence on the stability of two Floquet states when their Floquet energies (real part) encounter a direct or an avoided crossing at resonance. The effect of the amplitude of oscillation on the nature of crossing of Floquet energies is also discussed. It is found that by adiabatically changing the frequency and amplitude of the oscillation field, one can manipulate the stability of states in the well. By means of a discrete transform, the two models are shown to have exactly the same Floquet energy spectrum at the same oscillating amplitude and frequency. The equivalence of the models is also demonstrated by means of the principle of gauge invariance.Comment: 15 pages, 7 figure

Seeds of Change: Strategies for Food Security for the Inner City

The product of a year's work for six researchers, Seeds of Change is perhaps the most thorough documentation of an urban community's food system. Sections on hunger, nutrition, food industry, supermarket industry, communmity case study, farmers' markets, urban agriculture, joint ventures, and food policy councils