The TheLMA project: Multi-GPU Implementation of the Lattice Boltzmann Method

International audienceIn this paper, we describe the implementation of a multi-graphical processing unit (GPU) fluid flow solver based on the lattice Boltzmann method (LBM). The LBM is a novel approach in computational fluid dynamics, with numerous interesting features from a computational, numerical, and physical standpoint. Our program is based on CUDA and uses POSIX threads to manage multiple computation devices. Using recently released hardware, our solver may therefore run eight GPUs in parallel, which allows us to perform simulations at a rather large scale. Performance and scalability are excellent, the speedup over sequential implementations being at least of two orders of magnitude. In addition, we discuss tiling and communication issues for present and forthcoming implementations

The TheLMA project: a thermal lattice Boltzmann solver for the GPU

International audienceIn this paper, we consider the implementation of a thermal flow solver based on the lattice Boltzmann method (LBM) for graphics processing units (GPUs). We first describe the hybrid thermal LBM model implemented, and give a concise review of the CUDA technology. The specific issues that arise with LBM on GPUs are outlined. We propose an approach for efficient handling of the thermal part. Performance is close to optimum and is significantly better than the one of comparable CPU solvers. We validate our code by simulating the differentially heated cubic cavity (DHC). The computed results for steady flow patterns are in good agreement with previously published ones. Finally, we use our solver to study the phenomenology of transitional flows in the DHC

Real-time lattice boltzmann shallow waters method for breaking wave simulations

We present a new approach for the simulation of surfacebased fluids based in a hybrid formulation of Lattice Boltzmann Method for Shallow Waters and particle systems. The modified LBM can handle arbitrary underlying terrain conditions and arbitrary fluid depth. It also introduces a novel method for tracking dry-wet regions and moving boundaries. Dynamic rigid bodies are also included in our simulations using a two-way coupling. Certain features of the simulation that the LBM can not handle because of its heightfield nature, as breaking waves, are detected and automatically turned into splash particles. Here we use a ballistic particle system, but our hybrid method can handle more complex systems as SPH. Both the LBM and particle systems are implemented in CUDA, although dynamic rigid bodies are simulated in CPU. We show the effectiveness of our method with various examples which achieve real-time on consumer-level hardware.Peer ReviewedPostprint (author's final draft

Recent progress in the discovery of macrocyclic compounds as potential anti-infective therapeutics

Novel therapeutic strategies are urgently needed for the treatment of serious diseases caused by viral, bacterial and parasitic infections, because currently used drugs are facing the problem of rapidly emerging resistance. There is also an urgent need for agents that act on novel pathogen-specific targets, in order to expand the repertoire of possible therapies. The high throughput screening of diverse small molecule compound libraries has provided only a limited number of new lead series, and the number of compounds acting on novel targets is even smaller. Natural product screening has traditionally been very successful in the anti-infective area. Several successful drugs on the market as well as other compounds in clinical development are derived from natural products. Amongst these, many are macrocyclic compounds in the 1-2 kDa size range. This review will describe recent advances and novel drug discovery approaches in the anti-infective area, focusing on synthetic and natural macrocyclic compounds for which in vivo proof of concept has been established. The review will also highlight the Protein Epitope Mimetics (PEM) technology as a novel tool in the drug discovery process. Here the structures of naturally occurring antimicrobial and antiviral peptides and proteins are used as starting points to generate novel macrocyclic mimetics, which can be produced and optimized efficiently by combinatorial synthetic methods. Several recent examples highlight the great potential of the PEM approach in the discovery of new anti-infective agents

Towards surface quantum optics with Bose-Einstein condensates in evanescent waves

We present a surface trap which allows for studying the coherent interaction of ultracold atoms with evanescent waves. The trap combines a magnetic Joffe trap with a repulsive evanescent dipole potential. The position of the magnetic trap can be controlled with high precision which makes it possible to move ultracold atoms to the surface of a glass prism in a controlled way. The optical potential of the evanescent wave compensates for the strong attractive van der Waals forces and generates a potential barrier at only a few hundred nanometers from the surface. The trap is tested with Rb Bose-Einstein condensates (BEC), which are stably positioned at distances from the surfaces below one micrometer

Diffuse reflection of a Bose-Einstein condensate from a rough evanescent wave mirror

We present experimental results showing the diffuse reflection of a Bose-Einstein condensate from a rough mirror, consisting of a dielectric substrate supporting a blue-detuned evanescent wave. The scattering is anisotropic, more pronounced in the direction of the surface propagation of the evanescent wave. These results agree very well with theoretical predictions.Comment: submitted to J Phys B, 10 pages, 6 figure

A trapped-ion local field probe

We introduce a measurement scheme that utilizes a single ion as a local field probe. The ion is confined in a segmented Paul trap and shuttled around to reach different probing sites. By the use of a single atom probe, it becomes possible characterizing fields with spatial resolution of a few nm within an extensive region of millimeters. We demonstrate the scheme by accurately investigating the electric fields providing the confinement for the ion. For this we present all theoretical and practical methods necessary to generate these potentials. We find sub-percent agreement between measured and calculated electric field values

Hierarchical Hidden Markov Model in Detecting Activities of Daily Living in Wearable Videos for Studies of Dementia

International audienceThis paper presents a method for indexing activities of daily living in videos obtained from wearable cameras. In the context of dementia diagnosis by doctors, the videos are recorded at patients' houses and later visualized by the medical practitioners. The videos may last up to two hours, therefore a tool for an efficient navigation in terms of activities of interest is crucial for the doctors. The specific recording mode provides video data which are really difficult, being a single sequence shot where strong motion and sharp lighting changes often appear. Our work introduces an automatic motion based segmentation of the video and a video structuring approach in terms of activities by a hierarchical two-level Hidden Markov Model. We define our description space over motion and visual characteristics of video and audio channels. Experiments on real data obtained from the recording at home of several patients show the difficulty of the task and the promising results of our approach

Engineering Thermostability in Artificial Metalloenzymes to Increase Catalytic Activity

Protein engineering has shown widespread use in improving the industrial application of enzymes and broadening the conditions they are able to operate under by increasing their thermostability and solvent tolerance. Here, we show that protein engineering can be used to increase the thermostability of an artificial metalloenzyme. Thermostable variants of the human steroid carrier protein 2L, modified to bind a metal catalyst, were created by rational design using structural data and a 3DM database. These variants were tested to identify mutations that enhanced the stability of the protein scaffold, and a significant increase in melting temperature was observed with a number of modified metalloenzymes. The ability to withstand higher reaction temperatures resulted in an increased activity in the hydroformylation of 1-octene, with more than fivefold improvement in turnover number, whereas the selectivity for linear aldehyde remained high up to 80%

Observation of the thermal Casimir force

Quantum theory predicts the existence of the Casimir force between macroscopic bodies, due to the zero-point energy of electromagnetic field modes around them. This quantum fluctuation-induced force has been experimentally observed for metallic and semiconducting bodies, although the measurements to date have been unable to clearly settle the question of the correct low-frequency form of the dielectric constant dispersion (the Drude model or the plasma model) to be used for calculating the Casimir forces. At finite temperature a thermal Casimir force, due to thermal, rather than quantum, fluctuations of the electromagnetic field, has been theoretically predicted long ago. Here we report the experimental observation of the thermal Casimir force between two gold plates. We measured the attractive force between a flat and a spherical plate for separations between 0.7 $\mu$m and 7 $\mu$m. An electrostatic force caused by potential patches on the plates' surfaces is included in the analysis. The experimental results are in excellent agreement (reduced $\chi^2$ of 1.04) with the Casimir force calculated using the Drude model, including the T=300 K thermal force, which dominates over the quantum fluctuation-induced force at separations greater than 3 $\mu$m. The plasma model result is excluded in the measured separation range.Comment: 6 page