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.

Data assimilation for marine monitoring and prediction: The MERCATOR operational assimilation systems and the MERSEA developments

During the past 15 years, a number of initiatives have been undertaken at national level to develop ocean forecasting systems operating at regional and/or global scales. The co-ordination between these efforts has been organized internationally through the Global Ocean Data Assimilation Experiment (GODAE). The French MERCATOR project is one of the leading participants in GODAE. The MERCATOR systems routinely assimilate a variety of observations such as multi-satellite altimeter data, sea-surface temperature and in situ temperature and salinity profiles, focusing on high-resolution scales of the ocean dynamics. The assimilation strategy in MERCATOR is based on a hierarchy of methods of increasing sophistication including optimal interpolation, Kalman filtering and variational methods, which are progressively deployed through the Syst`eme d’Assimilation MERCATOR (SAM) series. SAM-1 is based on a reduced-order optimal interpolation which can be operated using ‘altimetry-only’ or ‘multi-data’ set-ups; it relies on the concept of separability, assuming that the correlations can be separated into a product of horizontal and vertical contributions. The second release, SAM-2, is being developed to include new features from the singular evolutive extended Kalman (SEEK) filter, such as three-dimensional, multivariate error modes and adaptivity schemes. The third one, SAM-3, considers variational methods such as the incremental four-dimensional variational algorithm. Most operational forecasting systems evaluated during GODAE are based on least-squares statistical estimation assuming Gaussian errors. In the framework of the EU MERSEA (Marine EnviRonment and Security for the European Area) project, research is being conducted to prepare the next-generation operational ocean monitoring and forecasting systems. The research effort will explore nonlinear assimilation formulations to overcome limitations of the current systems. This paper provides an overview of the developments conducted in MERSEA with the SEEK filter, the Ensemble Kalman filter and the sequential importance re-sampling filter.

The application of affine projection to the development of a siren noise cancellation system

Emergency vehicles use high-amplitude sirens to warn pedestrians and other road users of their presence. Unfortunately, the siren noise enters the vehicle and corrupts the intelligibility of two-way radio voice com-munications from the emergency vehicle to a control room. Often the siren has to be turned off to enable the control room to hear what is being said which subsequently endangers people's lives. A digital signal processing (DSP) based system for the cancellation of siren noise embedded within speech is presented. The system has been tested with the least mean square (LMS), normalised least mean square (NLMS) and affine projection algorithm (APA) using recordings from three common types of sirens (two-tone, wail and yelp) from actual test vehicles. It was found that the APA with a projection order of 2 gives comparably improved cancellation over the LMS and NLMS with only a moderate increase in algorithm complexity and code size. Therefore, this siren noise cancellation system using the APA offers an improvement in cancellation achieved by previous systems. The removal of the siren noise improves the response time for the emergency vehicle and thus the system can contribute to saving lives. The system also allows voice communication to take place even when the siren is on and as such the vehicle offers less risk of danger when moving at high speeds in heavy traffic.

Assessment of the RE(OH)3 Ising magnetic materials as possible candidates for the study of transverse-field-induced quantum phase transitions

The LiHoxY1−xF4 Ising magnetic material subject to a magnetic field perpendicular to the Ho3+ Ising direction has shown over the past 20 years to be a host of very interesting thermodynamic and magnetic phenomena. Unfortunately, the availability of other magnetic materials other than LiHoxY1−xF4 that may be described by a transverse-field Ising model remains very much limited. It is in this context that we use here a mean-field theory to investigate the suitability of the Ho(OH)3, Dy(OH)3, and Tb(OH)3 insulating hexagonal dipolar Ising-type ferromagnets for the study of the quantum phase transition induced by a magnetic field, Bx, applied perpendicular to the Ising spin direction. Experimentally, the zero-field critical (Curie) temperatures are known to be Tc≈2.54, 3.48, and 3.72 K, for Ho(OH)3, Dy(OH)3, and Tb(OH)3, respectively. From our calculations we estimate the critical transverse field, Bxc, to destroy ferromagnetic order at zero temperature to be Bxc=4.35, 5.03, and 54.81 T for Ho(OH)3, Dy(OH)3, and Tb(OH)3, respectively. We find that Ho(OH)3, similarly to LiHoF4, can be quantitatively described by an effective S=1/2 transverse-field Ising model. This is not the case for Dy(OH)3 due to the strong admixing between the ground doublet and first excited doublet induced by the dipolar interactions. Furthermore, we find that the paramagnetic (PM) to ferromagnetic (FM) transition in Dy(OH)3 becomes first order for strong Bx and low temperatures. Hence, the PM to FM zero-temperature transition in Dy(OH)3 may be first order and not quantum critical. We investigate the effect of competing antiferromagnetic nearest-neighbor exchange and applied magnetic field, Bz, along the Ising spin direction ẑ on the first-order transition in Dy(OH)3. We conclude from these preliminary calculations that Ho(OH)3 and Dy(OH)3 and their Y3+ diamagnetically diluted variants, HoxY1−x(OH)3 and DyxY1−x(OH)3, are potentially interesting systems to study transverse-field-induced quantum fluctuations effects in hard axis (Ising-type) magnetic materials.

Induced random fields in the LiHoxY1-xF4 quantum ising magnet in a transverse magnetic field

The LiHoxY1-xF4 magnetic material in a transverse magnetic field Bxx̂ perpendicular to the Ising spin direction has long been used to study tunable quantum phase transitions in a random disordered system. We show that the Bx-induced magnetization along the x̂ direction, combined with the local random dilution-induced destruction of crystalline symmetries, generates, via the predominant dipolar interactions between Ho3+ ions, random fields along the Ising ẑ direction. This identifies LiHoxY1-xF4 in Bx as a new random field Ising system. The random fields explain the rapid decrease of the critical temperature in the diluted ferromagnetic regime and the smearing of the nonlinear susceptibility at the spin-glass transition with increasing Bx and render the Bx-induced quantum criticality in LiHoxY1-xF4 likely inaccessible.

Some uniform stability and convergence results for integral equations on the real line and projection methods for their solution

The paper considers second kind equations of the form (abbreviated x=y + K2x) in which and the factor z is bounded but otherwise arbitrary so that equations of Wiener-Hopf type are included as a special case. Conditions on a set are obtained such that a generalized Fredholm alternative is valid: if W satisfies these conditions and I − Kz, is injective for each z ε W then I − Kz is invertible for each z ε W and the operators (I − Kz)−1 are uniformly bounded. As a special case some classical results relating to Wiener-Hopf operators are reproduced. A finite section version of the above equation (with the range of integration reduced to [−a, a]) is considered, as are projection and iterated projection methods for its solution. The operators (where denotes the finite section version of Kz) are shown uniformly bounded (in z and a) for all a sufficiently large. Uniform stability and convergence results, for the projection and iterated projection methods, are obtained. The argument generalizes an idea in collectively compact operator theory. Some new results in this theory are obtained and applied to the analysis of projection methods for the above equation when z is compactly supported and k(s − t) replaced by the general kernel k(s,t). A boundary integral equation of the above type, which models outdoor sound propagation over inhomogeneous level terrain, illustrates the application of the theoretical results developed.

Projection of global wave climate change towards the end of the 21st century

Wind generated waves at the sea surface are of outstanding importance for both their practical relevance in many aspects, such as coastal erosion, protection, or safety of navigation, and for their scientific relevance in modifying fluxes at the air-sea interface. So far long-term changes in ocean wave climate have been studied mostly from a regional perspective with global dynamical studies emerging only recently. Here a global wave climate study is presented, in which a global wave model (WAM) is driven by atmospheric forcing from a global climate model (ECHAM5) for present day and potential future climate conditions represented by the IPCC (Intergovernmental Panel for Climate Change) A1B emission scenario. It is found that changes in mean and extreme wave climate towards the end of the twenty-first century are small to moderate, with the largest signals being a poleward shift in the annual mean and extreme significant wave heights in the mid-latitudes of both hemispheres, more pronounced in the Southern Hemisphere, and most likely associated with a corresponding shift in mid-latitude storm tracks. These changes are broadly consistent with results from the few studies available so far. The projected changes in the mean wave periods, associated with the changes in the wave climate in the mid to high latitudes, are also shown, revealing a moderate increase in the equatorial eastern side of the ocean basins. This study presents a step forward towards a larger ensemble of global wave climate projections required to better assess robustness and uncertainty of potential future wave climate change.

Optimal convergence estimates for the trace of the polynomial L2-projection operator on a simplex

In this paper we study convergence of the L2-projection onto the space of polynomials up to degree p on a simplex in Rd, d >= 2. Optimal error estimates are established in the case of Sobolev regularity and illustrated on several numerical examples. The proof is based on the collapsed coordinate transform and the expansion into various polynomial bases involving Jacobi polynomials and their antiderivatives. The results of the present paper generalize corresponding estimates for cubes in Rd from [P. Houston, C. Schwab, E. Süli, Discontinuous hp-finite element methods for advection-diffusion-reaction problems. SIAM J. Numer. Anal. 39 (2002), no. 6, 2133-2163].

An integrated study of urban microclimates in Chongqing, China: historical weather data, transverse measurement and numerical simulation

Chongqing is the largest central-government-controlled municipality in China, which is now under going a rapid urbanization. The question remains open: What are the consequences of such rapid urbanization in Chongqing in terms of urban microclimates? An integrated study comprising three different research approaches is adopted in the present paper. By analyzing the observed annual climate data, an average rising trend of 0.10◦C/decade was found for the annual mean temperature from 1951 to 2010 in Chongqing,indicating a higher degree of urban warming in Chongqing. In addition, two complementary types of field measurements were conducted: fixed weather stations and mobile transverse measurement. Numerical simulations using a house-developed program are able to predict the urban air temperature in Chongqing.The urban heat island intensity in Chongqing is stronger in summer compared to autumn and winter.The maximum urban heat island intensity occurs at around midnight, and can be as high as 2.5◦C. In the day time, an urban cool island exists. Local greenery has a great impact on the local thermal environment.Urban green spaces can reduce urban air temperature and therefore mitigate the urban heat island. The cooling effect of an urban river is limited in Chongqing, as both sides of the river are the most developed areas, but the relative humidity is much higher near the river compared with the places far from it.

Thermal ion flows in the topside auroral ionosphere and the effects of low-altitude, transverse acceleration

Topside ionospheric profiles are used to study the upward field-aligned flow of thermal O+ at high latitudes. On the majority of the field lines outside the plasmasphere, the mean flux is approximately equal to the mean polar wind measured by spacecraft at greater altitudes. This is consistent with the theory of thermal light ion escape supported, via charge exchange, by upward O+ flow at lower heights. Events of larger O+ flow are detected at auroral latitudes and their occurrence is found to agree with that of transversely accelerated ions within the topside ionosphere and the magnetosphere. The effects of low altitude heating of O+ by oxygen cyclotron waves, driven by downward field-aligned currents, are considered as a possible common cause of these two types of event.