The structure of binary Lennard-Jones clusters: The effects of atomic size ratio

We introduce a global optimization approach for binary clusters that for a given cluster size is able to directly search for the structure and composition that has the greatest stability. We apply this approach to binary Lennard-Jones clusters, where the strength of the interactions between the two atom types is the same, but where the atoms have different sizes. We map out how the most stable structure depends on the cluster size and the atomic size ratio for clusters with up to 100 atoms and up to 30% difference in atom size. A substantial portion of this parameter space is occupied by structures that are polytetrahedral, both those that are polyicosahedral and those that involve disclination lines. Such structures involve substantial strains for one-component Lennard-Jones clusters, but can be stabilized by the different-sized atoms in the binary clusters. These structures often have a `core-shell' geometry, where the larger atoms are on the surface, and the smaller atoms are in the core.Comment: 13 pages, 9 figure

GPU driven finite difference WENO scheme for real time solution of the shallow water equations

The shallow water equations are applicable to many common engineering problems involving modelling of waves dominated by motions in the horizontal directions (e.g. tsunami propagation, dam breaks). As such events pose substantial economic costs, as well as potential loss of life, accurate real-time simulation and visualization methods are of great importance. For this purpose, we propose a new finite difference scheme for the 2D shallow water equations that is specifically formulated to take advantage of modern GPUs. The new scheme is based on the so-called Picard integral formulation of conservation laws combined with Weighted Essentially Non-Oscillatory reconstruction. The emphasis of the work is on third order in space and second order in time solutions (in both single and double precision). Further, the scheme is well-balanced for bathymetry functions that are not surface piercing and can handle wetting and drying in a GPU-friendly manner without resorting to long and specific case-by-case procedures. We also present a fast single kernel GPU implementation with a novel boundary condition application technique that allows for simultaneous real-time visualization and single precision simulations even on large ( > 2000 × 2000) grids on consumer-level hardware - the full kernel source codes are also provided online at https://github.com/pparna/swe_pifweno3

Small Engine Component Technology (SECT) studies

A study was conducted to identify component technology requirements for small, expendable gas turbine engines that would result in substantial improvements in performance and cost by the year 2000. A subsonic, 2600 nautical mile (4815 km) strategic cruise missile mission was selected for study. A baseline (state-of-the-art) engine and missile configuration were defined to evaluate the advanced technology engines. Two advanced technology engines were configured and evaluated using advanced component efficiencies and ceramic composite materials; a 22:1 overall pressure ratio, 3.85 bypass ratio twin-spool turbofan; and an 8:1 overall pressure, 3.66 bypass ratio, single-spool recuperated turbofan with 0.85 recuperator effectiveness. Results of mission analysis indicated a reduction in fuel burn of 38 and 47 percent compared to the baseline engine when using the advanced turbofan and recuperated turbofan, respectively. While use of either advanced engine resulted in approximately a 25 percent reduction in missile size, the unit life cycle (LCC) cost reduction of 56 percent for the advanced turbofan relative to the baseline engine gave it a decisive advantage over the recuperated turbofan with 47 percent LCC reduction. An additional range improvement of 10 percent results when using a 56 percent loaded carbon slurry fuel with either engine. These results can be realized only if significant progress is attained in the fields of solid lubricated bearings, small aerodynamic component performance, composite ceramic materials and integration of slurry fuels. A technology plan outlining prospective programs in these fields is presented

Interpreting two-photon imaging data of lymphocyte motility

Recently, using two-photon imaging it has been found that the movement of B and T cells in lymph nodes can be described by a random walk with persistence of orientation in the range of 2 minutes. We interpret this new class of lymphocyte motility data within a theoretical model. The model considers cell movement to be composed of the movement of subunits of the cell membrane. In this way movement and deformation of the cell are correlated to each other. We find that, indeed, the lymphocyte movement in lymph nodes can best be described as a random walk with persistence of orientation. The assumption of motility induced cell elongation is consistent with the data. Within the framework of our model the two-photon data suggest that T and B cells are in a single velocity state with large stochastic width. The alternative of three different velocity states with frequent changes of their state and small stochastic width is less likely. Two velocity states can be excluded

Cutting edge: back to "one-way" germinal centers

The present status of germinal center (GC) research is revisited using in silico simulations based on recent lymphocyte motility data in mice. The generally adopted view of several rounds of somatic hypermutations and positive selection is analyzed with special emphasis on the spatial organization of the GC reaction. We claim that the development of dark zones is not necessary for successful GC reactions to develop. We find that a recirculation of positively selected centrocytes to the dark zone is rather unlikely. Instead we propose a scenario that combines a multiple-step mutation and selection concept with a "one-way" GC in the sense of cell migration

An analysis of B cell selection mechanisms in germinal centres

Affinity maturation of antibodies during immune responses is achieved by multiple rounds of somatic hypermutation and subsequent preferential selection of those B cells that express B cell receptors with improved binding characteristics for the antigen. The mechanism underlying B cell selection has not yet been defined. By employing an agent-based model, we show that for physiologically reasonable parameter values affinity maturation can be driven by competition for neither binding sites nor antigen—even in the presence of competing secreted antibodies. Within the tested mechanisms, only clonal competition for T cell help or a refractory time for the interaction of centrocytes with follicular dendritic cells is found to enable affinity maturation while generating the experimentally observed germinal centre characteristics and tolerating large variations in the initial antigen density

Analysis of B cell selection mechanisms in the adaptive immune response

The essential task of a germinal centre reaction is the selection of those B cells that bind the antigen with high affinity. The exact mechanisms of B cell selection is still unknown and rather difficult to be accessed in experiment. With the help of an already established agent-based model for the space-time-dynamics of germinal centre reactions [1,2] we compare the most important hypotheses for what the limiting factor for B cell rescue may be. We discuss competition for antigen sites on follicular dendritic cells, a refractory time for centrocytes after every encounter with follicular dendritic cells, competition for the antigen itself, the role of antigen masking with soluble antibodies, and competition for T cell help. The unexpected result is that neither competition for interaction sites nor competition for antigen nor antigen masking are in agreement with present experimental data on germinal centre reactions. We show that these most popular selection mechanisms do not lead to sufficient affinity maturation and do not respect the observed robustness against changes of initial conditions. However, the best agreement with data was found for the newly hypothesized centrocyte refractory time and for competition for T cell help. Thus the in silico experiments point towards selection mechanisms that are not in the main focus of current germinal centre research. Possible experiments to test these hypotheses are proposed

High-performance liquid chromatography analysis of mezlocillin, piperacillin, their degradation products, and of ioxitalamic acid in plasma and urine of healthy volunteers

In plasma and urine of 10 healthy volunteers after intravenous administration of 4 g mezlocillin and piperacillin, respectively, the parent compounds as well as degradation products were assayed by high-performance liquid chromatography. Ioxitalamic acid, a renal contrast medium, was administered simultaneously, in order to measure the glomerular filtration rate, and to control the collection of 24-h urine. As metabolite of mezlocillin the corresponding penicilloic acid only was found, whereas in the case of piperacillin a further degradation product was observed. Half of the doses given was recovered in the urine as unchanged drugs, and in addition 5-10% as metabolites. No differences were found in the pharmacokinetic behaviour of both antibiotics

Revising old child support orders: The Wisconsin experience

In an effort to make Wisconsin's child support cases more equitable and up-to-date, child support staff reviewed "old" child support orders in thirteen of the state's seventy-two counties. (Reviewing old child support orders is now mandatory under the provisions of the Family Support Act of 1988.) Of the reviewed cases, only 21 percent were revised. Primary reasons for non-revision were the economic circumstances of the noncustodial parent (among welfare cases) and a lack of permission by the custodial parent to proceed (among non-welfare cases). Revised orders increased substantially, an average of $116/month (77 percent). An alternative method of keeping orders current is to express them as a percentage of the noncustodial parent's income; these orders are kept up-to-date automatically and are associated with large increases in collections.

Coarse Graining of Nonbonded Inter-particle Potentials Using Automatic Simplex Optimization to Fit Structural Properties

We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered in molecular dynamics simulations is reduced while conserving as many properties of the original substance as possible. We address the problem of finding nonbonded interaction parameters which reproduce structural properties from experiment or atomistic simulations. The approach consists of optimizing automatically nonbonded parameters using the simplex algorithm to fit structural properties like the radial distribution function as target functions. Moreover, any mix of structural and thermodynamic properties can be included in the target function. Different spherically symmetric inter-particle potentials are discussed. Besides demonstrating the method for Lennard--Jones liquids, it is applied to several more complex molecular liquids such as diphenyl carbonate, tetrahydrofurane, and monomers of poly(isoprene).Comment: 24 pages, 3 tables, 14 figures submitted to the Journal of Chemical Physics (JCP