The two-regime method for optimizing stochastic reaction–diffusion simulations

Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models. Often microscopic detail is only required in a small region (e.g. close to the cell membrane). Currently, the best way to achieve microscopic detail is to use a resource-intensive simulation over the whole domain. We develop the two-regime method (TRM) in which a molecular-based algorithm is used where desired and a compartment-based approach is used elsewhere. We present easy-to-implement coupling conditions which ensure that the TRM results have the same accuracy as a detailed molecular-based model in the whole simulation domain. Therefore, the TRM combines strengths of previously developed stochastic reaction–diffusion software to efficiently explore the behaviour of biological models. Illustrative examples and the mathematical justification of the TRM are also presented.     

Temperature‐Dependent Exciton and Trap‐Related Photoluminescence of CdTe Quantum Dots Embedded in a NaCl Matrix: Implication in Thermometry

Temperature‐dependent optical studies of semiconductor quantum dots (QDs) are fundamentally important for a variety of sensing and imaging applications. The steady‐state and time‐resolved photoluminescence properties of CdTe QDs in the size range from 2.3 to 3.1 nm embedded into a protective matrix of NaCl are studied as a function of temperature from 80 to 360 K. The temperature coefficient is found to be strongly dependent on QD size, with the highest sensitivity obtained for the smallest size of QDs. The emission from solid‐state CdTe QD‐based powders is maintained with high color purity over a wide range of temperatures. Photoluminescence lifetime data suggest that temperature dependence of the intrinsic radiative lifetime in CdTe QDs is rather weak, and it is mostly the temperature‐dependent nonradiative decay of CdTe QDs which is responsible for the thermal quenching of photoluminescence intensity. By virtue of the temperature‐dependent photoluminescence behavior, high color purity, photostability, and high photoluminescence quantum yield (26%–37% in the solid state), CdTe QDs embedded in NaCl matrices are useful solid‐state probes for thermal imaging and sensing over a wide range of temperatures within a number of detection schemes and outstanding sensitivity, such as luminescence thermochromic imaging, ratiometric luminescence, and luminescence lifetime thermal sensing.     

Higher‐order extensions of a discontinuous Galerkin method for mid‐frequency Helmholtz problems

Recently, a discontinuous Galerkin method with plane wave basis functions and Lagrange multiplier degrees of freedom was proposed for the efficient solution of Helmholtz problems in the mid‐frequency regime. In this paper, this method is extended to higher‐order elements. Performance results obtained for various two‐dimensional problems highlight the advantages of these elements over classical higher‐order Galerkin elements such as Q₂ and Q₄ for the discretization of interior and exterior Helmholtz problems. Copyright © 2004 John Wiley & Sons, Ltd.     

A hybrid discontinuous in space and time Galerkin method for wave propagation problems

Medium‐frequency regime and multi‐scale wave propagation problems have been a subject of active research in computational acoustics recently. New techniques have attempted to overcome the limitations of existing discretization methods that tend to suffer from dispersion. One such technique, the discontinuous enrichment method, incorporates features of the governing partial differential equation in the approximation, in particular, the solutions of the homogeneous form of the equation. Here, based on this concept and by extension of a conventional space–time finite element method, a hybrid discontinuous Galerkin method (DGM) for the numerical solution of transient problems governed by the wave equation in two and three spatial dimensions is described. The discontinuous formulation in both space and time enables the use of solutions to the homogeneous wave equation in the approximation. In this contribution, within each finite element, the solutions in the form of polynomial waves are employed. The continuity of these polynomial waves is weakly enforced through suitably chosen Lagrange multipliers. Results for two‐dimensional and three‐dimensional problems, in both low‐frequency and medium‐frequency regimes, show that the proposed DGM outperforms the conventional space–time finite element method. Copyright © 2014 John Wiley & Sons, Ltd.     

Dry versus hydrated collagen scaffolds: are dry states representative of hydrated states?

Collagen composite scaffolds have been used for a number of studies in tissue engineering. The hydration of such highly porous and hydrophilic structures may influence mechanical behaviour and porosity due to swelling. The differences in physical properties following hydration would represent a significant limiting factor for the seeding, growth and differentiation of cells in vitro and the overall applicability of such hydrophilic materials in vivo. Scaffolds based on collagen matrix, poly(DL-lactide) nanofibers, calcium phosphate particles and sodium hyaluronate with 8 different material compositions were characterised in the dry and hydrated states using X-ray microcomputed tomography, compression tests, hydraulic permeability measurement, degradation tests and infrared spectrometry. Hydration, simulating the conditions of cell seeding and cultivation up to 48?h and 576?h, was found to exert a minor effect on the morphological parameters and permeability. Conversely, hydration had a major statistically significant effect on the mechanical behaviour of all the tested scaffolds. The elastic modulus and compressive strength of all the scaffolds decreased by ~95%. The quantitative results provided confirm the importance of analysing scaffolds in the hydrated rather than the dry state since the former more precisely simulates the real environment for which such materials are designed.

Open image in new window

     

How to influence social policy affecting children and families.

Discusses recent legislative trends in child and family policy, sociopolitical forces behind those trends, and ways in which pro-children's groups can affect ongoing or future legislation. The effects of budget cuts in federal funding for daycare, child nutrition, and child support programs are described. It is asserted that, to make significant progress affecting children and families, a broader coalition of children's groups, encompassing members of both political parties and the interests of children whose mothers work at home and whose mothers are part of the work force, must be formed. Strong and effective federal agencies are needed to provide the focal point for developing and implementing policy. (6 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Off-line coupling of capillary electrophoresis to substrate-assisted laser desorption inductively coupled plasma mass spectrometry

A novel off-line coupling of capillary electrophoresis (CE) and inductively coupled plasma mass spectrometry (ICPMS) is reported here. The coupling interface is based on the connection of a separation capillary to a deposition capillary via a liquid junction maintaining high separation efficiency and sample utilization due to the self-focusing effect and lack of pressure-induced flow in comparison with nebulizer-like interfaces. The separation is recorded in the form of droplets of CE effluent on a suitable substrate--a poly(ethylene terephthalate) glycol (PETG) sample plate placed inside a partially evacuated chamber. Substrate-assisted laser desorption (SALD) is used to vaporize the sample fractions and to enable further transfer to the ICPMS. The mechanism of SALD is examined using model samples deposited on a variety of substrates. The highest response is obtained for a PETG substrate; sample desorption due to ablation of PETG is found to outweigh direct ablation of sample. Detection limits are given for several metal elements. Finally, a rapid (2.5-min), high-resolution separation of Cr(III)/Cr(VI) species injected in subpicomolar quantity is shown.