Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new ...methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) that combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.
Pharmacologic suppression of the effector phase ot contact hypersensitivity appears to have major relevance with regard to treatment of type IV reactions like contact dermatitis. Recently, tumor ...necrosis factor α has been shown to be a critical mediator in hapten-induced irritant and contact hypersensitivity reactions, thus offering new possibilities, for therapeutic intervention. Pentoxifylline, a methylxanthine derivative used in the treatment of vascular disorders, currently has been found to suppress the production of tumor necrosis factor α by human and murine leukocytes. Therefore, the effect of pentoxifylline on the elicitation phase of contact hypersensitivity was studied. Intraperitoneal injection of pentoxifylline into sensitized Balb/c and C3H/HeN mice before application of the challenging hapten dose resulted in a significant reduction of the outcome of the contact hypersensitivity reaction. The suppressive effect of pentoxifylline was dose dependent and maximally pronounced upon injection 3 h before hapten application. In contrast to the effector phase of contact hypersensitivity, induction of contact hypersensitivity was not affected by pentoxifylline when injected into naive mice before performance of sensitization. In addition, irritant dermatitis induced by 1% croton oil or 5% benzalkonium chloride was suppressed by pentoxifylline as well. These data suggest a potential pharmacologic intervention with pentoxifylline as a means to treat contact dermatitis.
Urban areas are heterogeneous. Transitions in architecture and building density, vegetation, economic activity, and culture can occur at the scale of city blocks. Ecologists have been criticized for ...treating the city as homogeneous and urbanization as one-dimensional. To develop ecological understanding of integrated human-natural systems, the fine-scale heterogeneity of their built and natural components must be quantified. There have been calls for the integration of the biophysical and human components of systems, but here we provide a new tool to quantify this integrated heterogeneity by reconceptualizing urban land-use and land-cover classification approaches. This new tool, High Ecological Resolution Classification for Urban Landscapes and Environmental Systems (HERCULES), balances detail and efficiency and is flexible, allowing it to be used for interdisciplinary research, with ancillary datasets, and across urban systems.
A curious feature of organ and organoid morphogenesis is that in certain cases, spatial oscillations in the thickness of the growing "film" are out of phase with the deformation of the slower-growing ..."substrate," while in other cases, the oscillations are in phase. The former cannot be explained by elastic bilayer instability, and contradict the notion that there is a universal mechanism by which brains, intestines, teeth, and other organs develop surface wrinkles and folds. Inspired by the microstructure of the embryonic cerebellum, we develop a new model of 2D morphogenesis in which system-spanning elastic fibers endow the organ with a preferred radius, while a separate fiber network resides in the otherwise fluidlike film at the outer edge of the organ and resists thickness gradients thereof. The tendency of the film to uniformly thicken or thin is described via a "growth potential." Several features of cerebellum, +blebbistatin organoid, and retinal fovea morphogenesis, including out-of-phase behavior and a film thickness amplitude that is comparable to the radius amplitude, are readily explained by our simple analytical model, as may be an observed scale invariance in the number of folds in the cerebellum. We also study a nonlinear variant of the model, propose further biological and bioinspired applications, and address how our model is and is not unique to the developing nervous system.
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) isolates have been the subject of numerous studies during recent years. The characterization of such isolates has usually ...also included the determination of their resistance phenotypes and associated resistance genotypes. Analysis of the resistance genes present in LA-MRSA isolates has revealed a number of genes commonly found in S. aureus and coagulase-negative staphylococci of humans and animals. In addition, novel resistance genes and/or resistance genes that have been rarely detected in staphylococci so far have been encountered. These include the phenicol exporter gene fexA, the multiresistance gene cfr, the tetracycline resistance gene tet(L), the trimethoprim resistance gene dfrK, the macrolide–lincosamide–streptogramin B resistance gene erm(T), the lincosamide–streptogramin A–pleuromutilin resistance genes vga(C) and vga(E), and the apramycin resistance gene apmA. Most of these genes were located on multiresistance plasmids in LA-MRSA. The co-localization of these resistance genes with other resistance genes enables their co-selection and persistence. LA-MRSA can therefore act as a donor and a recipient of antimicrobial resistance genes within the Gram-positive gene pool.
Delivering the full benefits of first-principles calculations to battery materials demands the development of accurate and computationally efficient electronic structure methods that incorporate the ...effects of the electrolyte environment and electrode potential. Realistic electrochemical interfaces containing polar surfaces are beyond the regime of validity of existing continuum solvation theories developed for molecules, due to the presence of significantly stronger electric fields. We present an ab initio theory of the nonlinear dielectric and ionic response of solvent environments within the framework of joint density-functional theory, with precisely the same optimizable parameters as conventional polarizable continuum models. We demonstrate that the resulting nonlinear theory agrees with the standard linear models for organic molecules and metallic surfaces under typical operating conditions. However, we find that the saturation effects in the rotational response of polar solvent molecules, inherent to our nonlinear theory, are crucial for a qualitatively correct description of the ionic surfaces typical of the solid electrolyte interface.
PDF
