Evaluation of the sea ice simulation in a new coupled atmosphere-ocean climate model (HadGEM1)

[ 1] A rapid increase in the variety, quality, and quantity of observations in polar regions is leading to a significant improvement in the understanding of sea ice dynamic and thermodynamic processes and their representation in global climate models. We assess the simulation of sea ice in the new Hadley Centre Global Environmental Model (HadGEM1) against the latest available observations. The HadGEM1 sea ice component uses elastic-viscous-plastic dynamics, multiple ice thickness categories, and zero-layer thermodynamics. The model evaluation is focused on the mean state of the key variables of ice concentration, thickness, velocity, and albedo. The model shows good agreement with observational data sets. The variability of the ice forced by the North Atlantic Oscillation is also found to agree with observations.

Evaluating a new LISFLOOD-FP formulation with data from the summer 2007 floods in Tewkesbury, UK

Two-dimensional flood inundation modelling is a widely used tool to aid flood risk management. In urban areas, where asset value and population density are greatest, the model spatial resolution required to represent flows through a typical street network (i.e. < 10m) often results in impractical computational cost at the whole city scale. Explicit diffusive storage cell models become very inefficient at such high resolutions, relative to shallow water models, because the stable time step in such schemes scales as a quadratic of resolution. This paper presents the calibration and evaluation of a recently developed new formulation of the LISFLOOD-FP model, where stability is controlled by the Courant–Freidrichs–Levy condition for the shallow water equations, such that, the stable time step instead scales linearly with resolution. The case study used is based on observations during the summer 2007 floods in Tewkesbury, UK. Aerial photography is available for model evaluation on three separate days from the 24th to the 31st of July. The model covered a 3.6 km by 2 km domain and was calibrated using gauge data from high flows during the previous month. The new formulation was benchmarked against the original version of the model at 20 m and 40 m resolutions, demonstrating equally accurate performance given the available validation data but at 67x faster computation time. The July event was then simulated at the 2 m resolution of the available airborne LiDAR DEM. This resulted in a significantly more accurate simulation of the drying dynamics compared to that simulated by the coarse resolution models, although estimates of peak inundation depth were similar.

Numerical simulation of the 12 May 1997 CME Event: The role of magnetic reconnection

We perform a numerical study of the evolution of a Coronal Mass Ejection (CME) and its interaction with the coronal magnetic field based on the 12 May 1997, CME event using a global MagnetoHydroDynamic (MHD) model for the solar corona. The ambient solar wind steady-state solution is driven by photospheric magnetic field data, while the solar eruption is obtained by superimposing an unstable flux rope onto the steady-state solution. During the initial stage of CME expansion, the core flux rope reconnects with the neighboring field, which facilitates lateral expansion of the CME footprint in the low corona. The flux rope field also reconnects with the oppositely orientated overlying magnetic field in the manner of the breakout model. During this stage of the eruption, the simulated CME rotates counter-clockwise to achieve an orientation that is in agreement with the interplanetary flux rope observed at 1 AU. A significant component of the CME that expands into interplanetary space comprises one of the side lobes created mainly as a result of reconnection with the overlying field. Within 3 hours, reconnection effectively modifies the CME connectivity from the initial condition where both footpoints are rooted in the active region to a situation where one footpoint is displaced into the quiet Sun, at a significant distance (≈1R ) from the original source region. The expansion and rotation due to interaction with the overlying magnetic field stops when the CME reaches the outer edge of the helmet streamer belt, where the field is organized on a global scale. The simulation thus offers a new view of the role reconnection plays in rotating a CME flux rope and transporting its footpoints while preserving its core structure.

Simulation of the impact of high temperature stress on annual crop yields

Brief periods of high temperature which occur near flowering can severely reduce the yield of annual crops such as wheat and groundnut. A parameterisation of this well-documented effect is presented for groundnut (i.e. peanut; Arachis hypogaeaL.). This parameterisation was combined with an existing crop model, allowing the impact of season-mean temperature, and of brief high-temperature episodes at various times near flowering, to be both independently and jointly examined. The extended crop model was tested with independent data from controlled environment experiments and field experiments. The impact of total crop duration was captured, with simulated duration being within 5% of observations for the range of season-mean temperatures used (20-28 degrees C). In simulations across nine differently timed high temperature events, eight of the absolute differences between observed and simulated yield were less than 10% of the control (no-stress) yield. The parameterisation of high temperature stress also allows the simulation of heat tolerance across different genotypes. Three parameter sets, representing tolerant, moderately sensitive and sensitive genotypes were developed and assessed. The new parameterisation can be used in climate change studies to estimate the impact of heat stress on yield. It can also be used to assess the potential for adaptation of cropping systems to increased temperature threshold exceedance via the choice of genotype characteristics. (c) 2005 Elsevier B.V. All rights reserved.

A novel parallel approach to the likelihood-based estimation of admixture in population genetics

Inferring population admixture from genetic data and quantifying it is a difficult but crucial task in evolutionary and conservation biology. Unfortunately state-of-the-art probabilistic approaches are computationally demanding. Effectively exploiting the computational power of modern multiprocessor systems can thus have a positive impact to Monte Carlo-based simulation of admixture modeling. A novel parallel approach is briefly described and promising results on its message passing interface (MPI)-based C implementation are reported.

The Origins of Lactase Persistence in Europe

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (-13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the -13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on -13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the -13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.

Accessing biodiversity resources in computational environments from workflow applications

In the Biodiversity World (BDW) project we have created a flexible and extensible Web Services-based Grid environment for biodiversity researchers to solve problems in biodiversity and analyse biodiversity patterns. In this environment, heterogeneous and globally distributed biodiversity-related resources such as data sets and analytical tools are made available to be accessed and assembled by users into workflows to perform complex scientific experiments. One such experiment is bioclimatic modelling of the geographical distribution of individual species using climate variables in order to predict past and future climate-related changes in species distribution. Data sources and analytical tools required for such analysis of species distribution are widely dispersed, available on heterogeneous platforms, present data in different formats and lack interoperability. The BDW system brings all these disparate units together so that the user can combine tools with little thought as to their availability, data formats and interoperability. The current Web Servicesbased Grid environment enables execution of the BDW workflow tasks in remote nodes but with a limited scope. The next step in the evolution of the BDW architecture is to enable workflow tasks to utilise computational resources available within and outside the BDW domain. We describe the present BDW architecture and its transition to a new framework which provides a distributed computational environment for mapping and executing workflows in addition to bringing together heterogeneous resources and analytical tools.

Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Design, synthesis and computational modelling of aromatic tweezer-molecules as models for chain-folding polymer blends

Novel 'tweezer-type' complexes that exploit the interactions between pi-electron-rich pyrenyl groups and pi-electron deficient diimide units have been designed and synthesised. The component molecules leading to complex formation were accessed readily from commercially available starting materials through short and efficient syntheses. Analysis of the resulting complexes, using the visible charge-transfer band, revealed association constants that increased sequentially from 130 to 11,000 M-1 as increasing numbers of pi-pi-stacking interactions were introduced into the systems. Computational modelling was used to analyse the structures of these complexes, revealing low-energy chain-folded conformations for both components, which readily allow close, multiple pi-pi-stacking and hydrogen bonding to be achieved. In this paper, we give details of our initial studies of these complexes and outline how their behaviour could provide a basis for designing self-healing polymer blends for use in adaptive coating systems. (C) 2008 Elsevier Ltd. All rights reserved.

Geometrical isomers of [TEAH][Co(L-Se)(2)]center dot xH(2)O: synthesis, structural, spectroscopic and computational studies

Trans-1, [HNEt3][Co-III(L-Se)(2)]center dot H2O and cis-1, [HNEt3][Co-III(L-Se)(2)]center dot 3H(2)O have been synthesized and characterized by single-crystal X-ray studies. The counter ion Et3NH+ plays a crucial role in the crystal packing leading to the formation of two distinctly different supramolecular assemblies in the two complexes. In trans-1, Co-bisphenolate units and triethylamine molecules are arranged in a linear fashion leading to a supramolecular columnar assembly along the crystallographic a-axis. In this assembly, triethylammonium ions are sandwiched between successive Co-bisphenolate units and act as gluing agents joining Co-bisphenolate units on either side through C-H center dot center dot center dot pi interactions. In sharp contrast to trans-1, Co-bisphenolate units and triethylammonium ions in cis-1 are arranged in a helical supramolecular assembly through similar C-H center dot center dot center dot pi interactions along the crystallographic b-axis. The Se center dot center dot center dot Se van der Waals interactions may be responsible for the predominant occurrence of the cis-isomer. The cyclic voltammetric studies showed quasi-reversible waves for the cobalt(III) -> cobalt(II) reductions with E-1/2 = 0.635 and 0.628 V vs. Ag/AgCl for cis-1 (at similar to 5 degrees C) and trans-1 (at similar to 25 degrees C), respectively. DFT calculations show that the trans-form is the thermodynamic product with higher stability than the cis-one, which is consistent with the variable temperature H-1 NMR studies

Discovery of three polymorphs of 7-fluoroisatin reveals challenges in using computational crystal structure prediction as a complement to experimental screening

A combined computational and experimental polymorph search was undertaken to establish the crystal forms of 7-fluoroisatin, a simple molecule with no reported crystal structures, to evaluate the value of crystal structure prediction studies as an aid to solid form discovery. Three polymorphs were found in a manual crystallisation screen, as well as two solvates. Form I ( P2(1)/c, Z0 1), found from the majority of solvent evaporation experiments, corresponded to the most stable form in the computational search of Z0 1 structures. Form III ( P21/ a, Z0 2) is probably a metastable form, which was only found concomitantly with form I, and has the same dimeric R2 2( 8) hydrogen bonding motif as form I and the majority of the computed low energy structures. However, the most thermodynamically stable polymorph, form II ( P1 , Z0 2), has an expanded four molecule R 4 4( 18) hydrogen bonding motif, which could not have been found within the routine computational study. The computed relative energies of the three forms are not in accord with experimental results. Thus, the experimental finding of three crystalline polymorphs of 7- fluoroisatin illustrates the many challenges for computational screening to be a tool for the experimental crystal engineer, in contrast to the results for an analogous investigation of 5- fluoroisatin.

E-commerce system simulation for construction and demolition waste exchange

This article introduces a quantitative approach to e-commerce system evaluation based on the theory of process simulation. The general concept of e-commerce system simulation is presented based on the considerations of some limitations in e-commerce system development such as the huge amount of initial investments of time and money, and the long period from business planning to system development, then to system test and operation, and finally to exact return; in other words, currently used system analysis and development method cannot tell investors about some keen attentions such as how good their e-commerce system could be, how many investment repayments they could have, and which area they should improve regarding the initial business plan. In order to exam the value and its potential effects of an e-commerce business plan, it is necessary to use a quantitative evaluation approach and the authors of this article believe that process simulation is an appropriate option. The overall objective of this article is to apply the theory of process simulation to e-commerce system evaluation, and the authors will achieve this though an experimental study on a business plan for online construction and demolition waste exchange. The methodologies adopted in this article include literature review, system analysis and development, simulation modelling and analysis, and case study. The results from this article include the concept of e-commerce system simulation, a comprehensive review of simulation methods adopted in e-commerce system evaluation, and a real case study of applying simulation to e-commerce system evaluation. Furthermore, the authors hope that the adoption and implementation of the process simulation approach can effectively support business decision-making, and improve the efficiency of e-commerce systems.

Performance evaluation of wall mounted convector for pre-heating naturally ventilated spaces

This paper presents the results of performance monitoring under real winter weather conditions, controlled laboratory testing and computational fluid dynamics (CFD) analysis of a wall mounted ventilation air inlet heat convector. For real winter weather monitoring, the wall-mounted convector was installed in a laboratory room of the Engineering Building of the School of Construction Management and Engineering. Air and hot water temperatures and air speeds were measured at the entrance to the convector and in the room. The hot water temperature was controlled at 40, 60 and 80 °C. The monitoring results were later used as boundary conditions for a CFD simulation to investigate the air movement in the room. Controlled laboratory testing was conducted in laboratories at the University of Reading, UK and at Wetterstad Consultancy, Sweden. The results of the performance investigation showed that the system contributed greatly to the room heating, particularly at a water temperature of 80 °C. Also adequate fresh air was supplied to the room. Such a system is able to provide an energy efficient method of eliminating problems associated with cold winter draughts.