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

Model Orchestration: Addressing the Model Management Challenges of Systems Biology

Biological modelling is an increasingly complex and diverse firld. As well as developing new models for biological phenomena, there is a need to integrate existing models and scale up to investigate higher level behaviour. To achieve this integration, techniques and tools are required to catalogue and understand existing models, and to support the development of new models ready for integration. We describe our approach to this problem and validate the approach with examples

OC-163 identification of inflammatory bowel disease (IBD) using field asymmetric ion mobility spectrometry (FAIMS)

Introduction Resident colonic bacteria, principally anaerobes and firmicutes, ferment undigested fibre. The resultant volatile organic compounds (VOCs) formed are dissolved in the faeces but also absorbed and excreted in the urine. We have previously shown that electronic nose (E-nose) analysis of urine VOCs distinguishes between Crohn's disease (CD), ulcerative colitis (UC) and healthy volunteers (HV): the underlying principle is pattern recognition of disease-specific “chemical fingerprint”. High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) offers a possible alternative. The underlying principle is separation of VOC chemical components based on their different ion mobilties in high electric fields. We performed a pilot study in the above groups, the patients in remission (Rem) or with active disease (AD), to assess if this technology could achieve separation between the groups. The results were validated against E-nose analysis. Methods 59 subjects were studied; HV n=14, UC (Rem) n=18, UC (AD) n=4; CD (Rem) n=19, CD (AD) n=4. Urine samples (7 ml) in universal containers (25 ml) were heated to 40±0.1 C. The headspace (the air above the sample) was then analysed using FAIMS. The data were analysed by Fisher Discriminant Analysis. Results The technique distinguished between the three groups. Additionally, patients with active disease could be distinguished from those in remission. These results were concordant with E-nose analysis. Conclusion This pilot shows that urine VOCs, analysed by the different approaches of E-nose and FAIMS, the latter a novel application, can distinguish the healthy from those with UC and CD when disease is active or in remission. The two technologies together offer a non-invasive approach to diagnosis and follow-up in inflammatory bowel disease

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

In situ measurements of density fluctuations and compressibility in silica glass as a function of temperature and thermal history

In this paper, small-angle X-ray scattering measurements are used to determine the different compressibility contributions, as well as the isothermal compressibility, in thermal equilibrium in silica glasses having different thermal histories. Using two different methods of analysis, in the supercooled liquid and in the glassy state, we obtain respectively the temperature and fictive temperature dependences of the isotheraml compressibility. The values obtained in the glass and supercooled liquid states are very close to each other. They agree with previous determinations of the literature. The compressibility in the glass state slightly decreases with increasing fictive temperature. The relaxational part of the compressibility is also calculated and compared to previous determinations. We discussed the small differences between the different determinations

From A to Z: Wearable technology explained

Wearable technology (WT) has become a viable means to provide low-cost clinically sensitive data for more informed patient assessment. The benefit of WT seems obvious: small, worn discreetly in any environment, personalised data and possible integration into communication networks, facilitating remote monitoring. Yet, WT remains poorly understood and technology innovation often exceeds pragmatic clinical demand and use. Here, we provide an overview of the common challenges facing WT if it is to transition from novel gadget to an efficient, valid and reliable clinical tool for modern medicine. For simplicity, an A–Z guide is presented, focusing on key terms, aiming to provide a grounded and broad understanding of current WT developments in healthcare

Testing the durability of limestone for Cathedral façade restoration

This research aimed to specify an optimum replacement stone for Truro Cathedral. A variety of petrographically and visually similar material to the original Bath stone was initially selected. The stones were subjected to three different durability tests; Sodium sulphate crystallisation and large scale testing with both accelerated and climatic freeze-thaw cyclic loading. The most suitable stone was determined as the one with the best performance characteristics overall

Characterization of the glass transition in vitreous silica by temperature scanning small-angle X-ray scattering

The temperature dependence of the x-ray scattering in the region below the first sharp diffraction peak was measured for silica glasses with low and high OH content (GE-124 and Corning 7980). Data were obtained upon scanning the temperature at 10, 40 and 80 K/min between 400 K and 1820 K. The measurements resolve, for the first time, the hysteresis between heating and cooling through the glass transition for silica glass, and the data have a better signal to noise ratio than previous light scattering and differential thermal analysis data. For the glass with the higher hydroxyl concentration the glass transition is broader and at a lower temperature. Fits of the data to the Adam-Gibbs-Fulcher equation provide updated kinetic parameters for this very strong glass. The temperature derivative of the observed X-ray scattering matches that of light scattering to within 14%.Comment: EurophysicsLetters, in pres