Immersive Projection for biochemical pattern matching

In all biological processes, protein molecules and other small molecules interact to function and form transient macromolecular complexes. This interaction of two or more molecules can be described by a docking event. Docking is an important phase for structure-based drug design strategies, as it can be used as a method to simulate protein-ligand interactions. Various docking programs exist that allow automated docking, but most of them have limited visualization and user interaction. It would be advantageous if scientists could visualize the molecules participating in the docking process, manipulate their structures and manually dock them before submitting the new conformations to an automated docking process in an immersive environment, which can help stimulate the design/docking process. This also could greatly reduce docking time and resources. To achieve this, we propose a new virtual modelling/docking program, whereby the advantages of virtual modelling programs and the efficiency of the algorithms in existing docking programs will be merged.

Detection of Parkinson’s disease tremor-onset with a frequency analysing artificial neural network

Deep Brain Stimulator devices are becoming widely used for therapeutic benefits in movement disorders such as Parkinson's disease. Prolonging the battery life span of such devices could dramatically reduce the risks and accumulative costs associated with surgical replacement. This paper demonstrates how an artificial neural network can be trained using pre-processing frequency analysis of deep brain electrode recordings to detect the onset of tremor in Parkinsonian patients. Implementing this solution into an 'intelligent' neurostimulator device will remove the need for continuous stimulation currently used, and open up the possibility of demand-driven stimulation. Such a methodology could potentially decrease the power consumption of a deep brain pulse generator.

The frequency and dynamics of stratospheric sudden warmings in the 21st century

Changes to stratospheric sudden warmings (SSWs) over the coming century, as predicted by the Geophysical Fluid Dynamics Laboratory (GFDL) chemistry climate model [Atmospheric Model With Transport and Chemistry (AMTRAC)], are investigated in detail. Two sets of integrations, each a three-member ensemble, are analyzed. The first set is driven with observed climate forcings between 1960 and 2004; the second is driven with climate forcings from a coupled model run, including trace gas concentrations representing a midrange estimate of future anthropogenic emissions between 1990 and 2099. A small positive trend in the frequency of SSWs is found. This trend, amounting to 1 event/decade over a century, is statistically significant at the 90% confidence level and is consistent over the two sets of model integrations. Comparison of the model SSW climatology between the late 20th and 21st centuries shows that the increase is largest toward the end of the winter season. In contrast, the dynamical properties are not significantly altered in the coming century, despite the increase in SSW frequency. Owing to the intrinsic complexity of our model, the direct cause of the predicted trend in SSW frequency remains an open question.

A Possible Influence of Equatorial Winds on the September 2002 Southern Hemisphere Sudden Warming Event

The stratospheric sudden warming in the Southern Hemisphere (SH) in September 2002 was unexpected for two reasons. First, planetary wave activity in the Southern Hemisphere is very weak, and midwinter warmings have never been observed, at least not since observations of the upper stratosphere became regularly available. Second, the warming occurred in a west phase of the quasi-biennial oscillation (QBO) in the lower stratosphere. This is unexpected because warmings are usually considered to be more likely in the east phase of the QBO, when a zero wind line is present in the winter subtropics and hence confines planetary wave propagation to higher latitudes closer to the polar vortex. At first, this evidence suggests that the sudden warming must therefore be simply a result of anomalously strong planetary wave forcing from the troposphere. However, recent model studies have suggested that the midwinter polar vortex may also be sensitive to the equatorial winds in the upper stratosphere, the region dominated by the semiannual oscillation. In this paper, the time series of equatorial zonal winds from two different data sources, the 40-yr ECMWF Re-Analysis (ERA) and the Met Office assimilated dataset, are reviewed. Both suggest that the equatorial winds in the upper stratosphere above 10 hPa were anomalously easterly in 2002. Idealized model experiments are described in which the modeled equatorial winds were relaxed toward these observations for various years to examine whether the anomalous easterlies in 2002 could influence the timing of a warming event. It is found that the 2002 equatorial winds speed up the evolution of a warming event in the model. Therefore, this study suggests that the anomalous easterlies in the 1–10-hPa region may have been a contributory factor in the development of the observed SH warming. However, it is concluded that it is unlikely that the anomalous equatorial winds alone can explain the 2002 warming event.

Modelling the hydraulics of the Carlisle 2005 flood event

The performance of a 2D numerical model of flood hydraulics is tested for a major event in Carlisle, UK, in 2005. This event is associated with a unique data set, with GPS surveyed wrack lines and flood extent surveyed 3 weeks after the flood. The Simple Finite Volume (SFV) model is used to solve the 2D Saint-Venant equations over an unstructured mesh of 30000 elements representing channel and floodplain, and allowing detailed hydraulics of flow around bridge piers and other influential features to be represented. The SFV model is also used to corroborate flows recorded for the event at two gauging stations. Calibration of Manning's n is performed with a two stage strategy, with channel values determined by calibration of the gauging station models, and floodplain values determined by optimising the fit between model results and observed water levels and flood extent for the 2005 event. RMS error for the calibrated model compared with surveyed water levels is ~±0.4m, the same order of magnitude as the estimated error in the survey data. The study demonstrates the ability of unstructured mesh hydraulic models to represent important hydraulic processes across a range of scales, with potential applications to flood risk management.

Jupiter's and Saturn's convectively driven banded jets in the laboratory

The banded patterns of cloud and wind are among the most striking features of the atmospheres of Jupiter and Saturn, but their dynamical origin remains poorly understood. Most approaches towards understanding zonation so far (also in the terrestrial oceans) have used highly idealized models to show that it might originate from dynamical anisotropy in a shallow turbulent fluid layer due to the planetary β-effect. Here we report the results of laboratory experiments, conducted on a 14-m diameter turntable, which quantitatively confirm that multiple zonal jets may indeed be generated and maintained by this mechanism in the presence of deep convection and a topographic β-effect. At the very small values of Ekman number (≤2 × 10−5) and large local Reynolds numbers (≥2000, based on jet scales) achieved, the kinetic energy spectra suggest the presence of both energy-cascading and enstrophy-cascading inertial ranges in addition to the zonation near twice the Rhines wave number.

Modelling European winter wind storm losses in current and future climate

Severe wind storms are one of the major natural hazards in the extratropics and inflict substantial economic damages and even casualties. Insured storm-related losses depend on (i) the frequency, nature and dynamics of storms, (ii) the vulnerability of the values at risk, (iii) the geographical distribution of these values, and (iv) the particular conditions of the risk transfer. It is thus of great importance to assess the impact of climate change on future storm losses. To this end, the current study employs—to our knowledge for the first time—a coupled approach, using output from high-resolution regional climate model scenarios for the European sector to drive an operational insurance loss model. An ensemble of coupled climate-damage scenarios is used to provide an estimate of the inherent uncertainties. Output of two state-of-the-art global climate models (HadAM3, ECHAM5) is used for present (1961–1990) and future climates (2071–2100, SRES A2 scenario). These serve as boundary data for two nested regional climate models with a sophisticated gust parametrizations (CLM, CHRM). For validation and calibration purposes, an additional simulation is undertaken with the CHRM driven by the ERA40 reanalysis. The operational insurance model (Swiss Re) uses a European-wide damage function, an average vulnerability curve for all risk types, and contains the actual value distribution of a complete European market portfolio. The coupling between climate and damage models is based on daily maxima of 10 m gust winds, and the strategy adopted consists of three main steps: (i) development and application of a pragmatic selection criterion to retrieve significant storm events, (ii) generation of a probabilistic event set using a Monte-Carlo approach in the hazard module of the insurance model, and (iii) calibration of the simulated annual expected losses with a historic loss data base. The climate models considered agree regarding an increase in the intensity of extreme storms in a band across central Europe (stretching from southern UK and northern France to Denmark, northern Germany into eastern Europe). This effect increases with event strength, and rare storms show the largest climate change sensitivity, but are also beset with the largest uncertainties. Wind gusts decrease over northern Scandinavia and Southern Europe. Highest intra-ensemble variability is simulated for Ireland, the UK, the Mediterranean, and parts of Eastern Europe. The resulting changes on European-wide losses over the 110-year period are positive for all layers and all model runs considered and amount to 44% (annual expected loss), 23% (10 years loss), 50% (30 years loss), and 104% (100 years loss). There is a disproportionate increase in losses for rare high-impact events. The changes result from increases in both severity and frequency of wind gusts. Considerable geographical variability of the expected losses exists, with Denmark and Germany experiencing the largest loss increases (116% and 114%, respectively). All countries considered except for Ireland (−22%) experience some loss increases. Some ramifications of these results for the socio-economic sector are discussed, and future avenues for research are highlighted. The technique introduced in this study and its application to realistic market portfolios offer exciting prospects for future research on the impact of climate change that is relevant for policy makers, scientists and economists.

The Upper Valanginian (Early Cretaceous) positive carbon-isotope event recorded in terrestrial plants

Our understanding of the ancient ocean-atmosphere system has focused on oceanic proxies. However, the study of terrestrial proxies is equally necessary to constrain our understanding of ancient climates and linkages between the terrestrial and oceanic carbon reservoirs. We have analyzed carbon-isotope ratios from fossil plant material through the Valanginian and Lower Hauterivian from a shallow-marine, ammonite-constrained succession in the Crimean Peninsula of the southern Ukraine in order to determine if the Upper Valanginian positive carbon-isotope excursion is expressed in the atmosphere. delta(13)C(plant) values fluctuate around -23% to -22% for the Valanginian-Hauterivian, except during the Upper Valanginian where delta(13)C(plant) values record a positive excursion to similar to-18%. Based upon ammonite biostratigraphy from Crimea, and in conjunction with a composite Tethyan marine delta(13)C(carb) curve, several conclusions can be drawn: (1) the delta(13)C(plant) record indicates that the atmospheric carbon reservoir was affected; (2) the defined ammonite correlations between Europe and Crimea are synchronous; and (3) a change in photosynthetic carbon-isotope fractionation, caused by a decrease in atmospheric PCO2, occurred during the Upper Valanginian Positive delta(13)C excursion. Our new data, combined with other paleoenvironmental and paleoclimatic information, indicate that the Upper Valanginian was a cool period (icehouse) and highlights that the Cretaceous period was interrupted by periods of cooling and was not an equable climate as previously thought. (C) 2005 Elsevier B.V. All rights reserved.

Influence of the seasonal cycle on the termination of El Nino events in a coupled general circulation model

In this study, the mechanisms leading to the El Nino peak and demise are explored through a coupled general circulation model ensemble approach evaluated against observations. The results here suggest that the timing of the peak and demise for intense El Nino events is highly predictable as the evolution of the coupled system is strongly driven by a southward shift of the intense equatorial Pacific westerly anomalies during boreal winter. In fact, this systematic late-year shift drives an intense eastern Pacific thermocline shallowing, constraining a rapid El Nino demise in the following months. This wind shift results from a southward displacement in winter of the central Pacific warmest SSTs in response to the seasonal evolution of solar insolation. In contrast, the intensity of this seasonal feedback mechanism and its impact on the coupled system are significantly weaker in moderate El Nino events, resulting in a less pronounced thermocline shallowing. This shallowing transfers the coupled system into an unstable state in spring but is not sufficient to systematically constrain the equatorial Pacific evolution toward a rapid El Nino termination. However, for some moderate events, the occurrence of intense easterly wind anomalies in the eastern Pacific during that period initiate a rapid surge of cold SSTs leading to La Nina conditions. In other cases, weaker trade winds combined with a slightly deeper thermocline allow the coupled system to maintain a broad warm phase evolving through the entire spring and summer and a delayed El Nino demise, an evolution that is similar to the prolonged 1986/87 El Nino event. La Nina events also show a similar tendency to peak in boreal winter, with characteristics and mechanisms mainly symmetric to those described for moderate El Nino cases.

Cone model-based SEP event calculations for applications to multipoint observations

The problem of modeling solar energetic particle (SEP) events is important to both space weather research and forecasting, and yet it has seen relatively little progress. Most important SEP events are associated with coronal mass ejections (CMEs) that drive coronal and interplanetary shocks. These shocks can continuously produce accelerated particles from the ambient medium to well beyond 1 AU. This paper describes an effort to model real SEP events using a Center for Integrated Space weather Modeling (CISM) MHD solar wind simulation including a cone model of CMEs to initiate the related shocks. In addition to providing observation-inspired shock geometry and characteristics, this MHD simulation describes the time-dependent observer field line connections to the shock source. As a first approximation, we assume a shock jump-parameterized source strength and spectrum, and that scatter-free transport occurs outside of the shock source, thus emphasizing the role the shock evolution plays in determining the modeled SEP event profile. Three halo CME events on May 12, 1997, November 4, 1997 and December 13, 2006 are used to test the modeling approach. While challenges arise in the identification and characterization of the shocks in the MHD model results, this approach illustrates the importance to SEP event modeling of globally simulating the underlying heliospheric event. The results also suggest the potential utility of such a model for forcasting and for interpretation of separated multipoint measurements such as those expected from the STEREO mission.