Computational challenges of systems biology

Progress in the study of biological systems such as the heart, brain, and liver will require computer scientists to work closely with life scientists and mathematicians. Computer science will play a key role in shaping the new discipline of systems biology and addressing the significant computational challenges it poses

Analyzing and Modeling the Performance of the HemeLB Lattice-Boltzmann Simulation Environment

We investigate the performance of the HemeLB lattice-Boltzmann simulator for cerebrovascular blood flow, aimed at providing timely and clinically relevant assistance to neurosurgeons. HemeLB is optimised for sparse geometries, supports interactive use, and scales well to 32,768 cores for problems with ~81 million lattice sites. We obtain a maximum performance of 29.5 billion site updates per second, with only an 11% slowdown for highly sparse problems (5% fluid fraction). We present steering and visualisation performance measurements and provide a model which allows users to predict the performance, thereby determining how to run simulations with maximum accuracy within time constraints.Comment: Accepted by the Journal of Computational Science. 33 pages, 16 figures, 7 table

Random walks near Rokhsar-Kivelson points

There is a class of quantum Hamiltonians known as Rokhsar-Kivelson(RK)-Hamiltonians for which static ground state properties can be obtained by evaluating thermal expectation values for classical models. The ground state of an RK-Hamiltonian is known explicitly, and its dynamical properties can be obtained by performing a classical Monte Carlo simulation. We discuss the details of a Diffusion Monte Carlo method that is a good tool for studying statics and dynamics of perturbed RK-Hamiltonians without time discretization errors. As a general result we point out that the relation between the quantum dynamics and classical Monte Carlo simulations for RK-Hamiltonians follows from the known fact that the imaginary-time evolution operator that describes optimal importance sampling, in which the exact ground state is used as guiding function, is Markovian. Thus quantum dynamics can be studied by a classical Monte Carlo simulation for any Hamiltonian that is free of the sign problem provided its ground state is known explicitly.Comment: 12 pages, 9 figures, RevTe

Dialogue and materiality/embodiment in science|arts creative pedagogy: their role and manifestation

This is the final version. Available on open access from Elsevier via the DOI in this record.This paper responds to recent calls to explore the nuances of the interaction between the sciences, the arts and their inherent creativity to better understand their potential within teaching and learning. Building on previous arguments that the science-arts-creativity relationship is dialogic and relational, this research focuses on the question: How are dialogue and material/embodied activity manifested within creative pedagogy? We begin with a fusion of Bakhtinian-inspired and New-Materialist understandings of dialogue drawing out the importance of embodiment in order to revitalize how we articulate dialogue within creative educational practice. We then take on the challenge of a materialist diffractive analysis to conduct research which complements the theoretical framing and offers our outcomes in a way that appropriately makes the phenomena tangible. We present the outcomes of the diffractive analysis including the constitution of matter as well as meaning in the dialogic space; and the emergence of new assemblages of embodied teachers, students, ideas, and objects within transdisciplinary educational practice. We conclude by arguing for the benefits of diffractive analysis: that we have fore-fronted the entangled relationality of trans-disciplinary creative pedagogy; avoided bracketing out aspects of education that are often side-lined; opened out the space of pedagogical approaches that might be attempted; and begun to challenge what education is for. In so doing, the article aims to open up new ways for teachers, students and researchers to experience seeing, doing, feeling and researching science|arts creative pedagogy and provoke conversations about how this might develop in the future.European Commissio

Building Community and Fostering Health and Well-Being through a Collaborative School Based Project

This article presents lessons learned from collaborative service-learning projects aimed at bridging the gap between theory and practice by providing students design experiences in authentic settings. Interior design students gained disciplinary and civic benefits while problem solving for a preK-5 elementary school calming room, dining room, and teacher sanctuary. The elementary school teachers and staff reported the redesigned calming room supported students’ emotional and self-regulation skills. Teachers and staff also reported the dining room and teacher sanctuary supported the school community well-being. The authors’ present findings and hope the article can serve as a model for educators interested in community building service-learning projects in school environments

A Natural Framework for Solar and 17 keV Neutrinos

Motivated by recent experimental claims for the existence of a 17 keV neutrino and by the solar neutrino problem, we construct a class of models which contain in their low-energy spectrum a single light sterile neutrino and one or more Nambu-Goldstone bosons. In these models the required pattern of breaking of lepton-number symmetry takes place near the electroweak scale and all mass heirarchies are technically natural. The models are compatible with all cosmological and astrophysical constraints, and can solve the solar neutrino problem via either the MSW effect or vacuum oscillations. The deficit in atmospheric muon neutrinos seen in the Kamiokande and IMB detectors can also be explained in these models.Comment: 23 page

Impact of blood rheology on wall shear stress in a model of the middle cerebral artery

Perturbations to the homeostatic distribution of mechanical forces exerted by blood on the endothelial layer have been correlated with vascular pathologies including intracranial aneurysms and atherosclerosis. Recent computational work suggests that in order to correctly characterise such forces, the shear-thinning properties of blood must be taken into account. To the best of our knowledge, these findings have never been compared against experimentally observed pathological thresholds. In the current work, we apply the three-band diagram (TBD) analysis due to Gizzi et al. to assess the impact of the choice of blood rheology model on a computational model of the right middle cerebral artery. Our results show that, in the model under study, the differences between the wall shear stress predicted by a Newtonian model and the well known Carreau-Yasuda generalized Newtonian model are only significant if the vascular pathology under study is associated with a pathological threshold in the range 0.94 Pa to 1.56 Pa, where the results of the TBD analysis of the rheology models considered differs. Otherwise, we observe no significant differences.Comment: 14 pages, 6 figures, published at Interface Focu

Wearable Haptic Devices for Gait Re-education by Rhythmic Haptic Cueing

This research explores the development and evaluation of wearable haptic devices for gait sensing and rhythmic haptic cueing in the context of gait re-education for people with neurological and neurodegenerative conditions. Many people with long-term neurological and neurodegenerative conditions such as Stroke, Brain Injury, Multiple Sclerosis or Parkinson’s disease suffer from impaired walking gait pattern. Gait improvement can lead to better fluidity in walking, improved health outcomes, greater independence, and enhanced quality of life. Existing lab-based studies with wearable devices have shown that rhythmic haptic cueing can cause immediate improvements to gait features such as temporal symmetry, stride length, and walking speed. However, current wearable systems are unsuitable for self-managed use for in-the-wild applications with people having such conditions. This work aims to investigate the research question of how wearable haptic devices can help in long-term gait re-education using rhythmic haptic cueing. A longitudinal pilot study has been conducted with a brain trauma survivor, providing rhythmic haptic cueing using a wearable haptic device as a therapeutic intervention for a two-week period. Preliminary results comparing pre and post-intervention gait measurements have shown improvements in walking speed, temporal asymmetry, and stride length. The pilot study has raised an array of issues that require further study. This work aims to develop and evaluate prototype systems through an iterative design process to make possible the self-managed use of such devices in-the-wild. These systems will directly provide therapeutic intervention for gait re-education, offer enhanced information for therapists, remotely monitor dosage adherence and inform treatment and prognoses over the long-term. This research will evaluate the use of technology from the perspective of multiple stakeholders, including clinicians, carers and patients. This work has the potential to impact clinical practice nationwide and worldwide in neuro-physiotherapy

Abnormal morphology biases haematocrit distribution in tumour vasculature and contributes to heterogeneity in tissue oxygenation

Oxygen heterogeneity in solid tumors is recognized as a limiting factor for therapeutic efficacy. This heterogeneity arises from the abnormal vascular structure of the tumor, but the precise mechanisms linking abnormal structure and compromised oxygen transport are only partially understood. In this paper, we investigate the role that red blood cell (RBC) transport plays in establishing oxygen heterogeneity in tumor tissue. We focus on heterogeneity driven by network effects, which are challenging to observe experimentally due to the reduced fields of view typically considered. Motivated by our findings of abnormal vascular patterns linked to deviations from current RBC transport theory, we calculated average vessel lengths L⎯⎯ and diameters d⎯⎯ from tumor allografts of three cancer cell lines and observed a substantial reduction in the ratio λ=L⎯⎯/d⎯⎯ compared to physiological conditions. Mathematical modeling reveals that small values of the ratio λ (i.e., λ<6 ) can bias hematocrit distribution in tumor vascular networks and drive heterogeneous oxygenation of tumor tissue. Finally, we show an increase in the value of λ in tumor vascular networks following treatment with the antiangiogenic cancer agent DC101. Based on our findings, we propose λ as an effective way of monitoring the efficacy of antiangiogenic agents and as a proxy measure of perfusion and oxygenation in tumor tissue undergoing antiangiogenic treatment

SMILE soft X-ray Imager flight model CCD370 pre-flight device characterisation

Throughout the SMILE mission the satellite will be bombarded by radiation which gradually damages the focal plane devices and degrades their performance. In order to understand the changes of the CCD370s within the soft X-ray Imager, an initial characterisation of the devices has been carried out to give a baseline performance level. Three CCDs have been characterised, the two flight devices and the flight spare. This has been carried out at the Open University in a bespoke cleanroom measurement facility. The results show that there is a cluster of bright pixels in the flight spare which increases in size with temperature. However at the nominal operating temperature (−120 °C) it is within the procurement specifications. Overall, the devices meet the specifications when operating at −120 °C in 6 × 6 binned frame transfer science mode. The serial charge transfer inefficiency degrades with temperature in full frame mode. However any charge losses are recovered when binning/frame transfer is implemented