Mechanical stimuli in energetic materials initiate chemical reactions at shock fronts prior to detonation. Shock sensitivity measurements provide widely varying results, and quantum-mechanical calculations are unable to handle systems large enough to describe shock structure. Recent developments in reactive forcefield molecular dynamics (REAXFF-MD) combined with advances in parallel computing have paved the way to accurately simulate reaction pathways along with the structure of shock fronts. Our multimillionatom REAXFF-MD simulations of l,3,5-trinitro-l,3,5-triazine (RDX) reveal that detonation is preceded by a transition from a diffuse shock front with well-ordered molecular dipoles behind it to a disordered dipole distribution behind a sharp front. [12 -14]. A major unsolved problem in this area of mechanochemistry is how strains trigger chemical reactions that cause detonation. Recently, the role of a mechanical stimulus, such as bond bending, in initiating reaction at a shock front has attracted much attention. Manna et al. have shown on the basis of density functional calculation of a TATB crystal that bond-bending of nitro group in TATB molecule closes the HOMO-LUMO gap and have speculated that reaction may proceed at supersonic speed [15]. Atomistic-level understanding of the structure of shock fronts at the onset of detonation requires multimillion-atom simulations with reaction chemistry under high strain rate deformations.We have performed a series of molecular dynamics (MD) simulations of planar shock on a slab of an l,3,5-trinitro-l,3,5-triazine (RDX) [16,17] crystal. Each RDX molecule consists of 21 atoms [ Fig. 1(a)], and the unit cell of the RDX crystal contains 8 RDX molecules [ Fig. 1(b)]. The x, y, and z axes are aligned with the [100], [010], and [001] crystallographic orientations, respectively. We apply periodic boundary conditions in all directions after adding 2 nm of vacuum layers on both sides of the slab along the x axis. We have simulated a system of N 2 322 432 atoms with dimensions 318:48 284:08 271:76 A 3 and also a system of 145 152 atoms to confirm that major results do not change with the system size. Initially, the system is relaxed for 1 ps at 5 K and then quenched to 0 K.Simulations reported here are based on a scalable implementation of a reactive force-field (REAXFF) MD [18,19] on massively parallel computers [20]. The REAXFF potential energy function consists of bonding and nonbonding interactions. Bonding interactions comprise coordination energy, two-body stretching, three-body bending and fourbody torsion energy functions. Nonbonding interactions consists of van der Waals and Coulomb energies [21], where charge transfer is included by an electronegativity FIG. 1 (color). (a) An RDX molecule with carbon (yellow), hydrogen (white), oxygen (red), and nitrogen (blue) atoms. (b) The unit cell of an RDX crystal contains 8 RDX molecules, which are colored blue and red depending on whether the NO 2 groups faces away from (group 1) or faces towards (group 2) the shock plane. Th...

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Abstract. Mast cell tumors (MCTs) of gastrointestinal origin that had been surgically removed from 39 dogs were examined to evaluate their pathologic features. Miniature breeds, especially Maltese, were most frequently affected. The average age of affected dogs was 9.7 Ϯ 2.6 years. No sex difference was apparent. The most frequently affected sites were in the upper digestive tract, and the prognosis was very poor. Grossly, the gastrointestinal wall was prominently thickened, and the lumen of the affected gut was usually narrowed. Microscopically, there was diffuse transmural invasion of round to pleomorphic tumor cells. Tumor cells had moderate to abundant cytoplasm, round to ovoid nuclei with scattered chromatin, and mitotic figures. Fibrous stroma was observed in about half of the tumors. There was variable infiltration of eosinophils. In all tumors, cytoplasmic granules showed weak metachromasia, but the number of granules was very small. Immunohistochemical staining for c-kit and mast cell tryptase was positive in 77% and 62% of tumors, respectively. All tumors were positive for at least two of these markers. Immunohistochemical staining for p53 was positive in 13% of the tumors. Reactivity for staining markers and p53 was unrelated to cell pleomorphism, vessel invasion, or survival time. Gastrointestinal MCTs have histologic and immunohistochemical features completely different from those of other primary or metastatic gastrointestinal tumors. The combination of immunostaining for mast cell tryptase and c-kit and histochemical staining for metachromasia appears to be a powerful tool for the diagnosis of gastrointestinal MCTs.

Impurities segregated to grain boundaries of a material essentially alter its fracture behavior. A prime example is sulfur segregation-induced embrittlement of nickel, where an observed relation between sulfur-induced amorphization of grain boundaries and embrittlement remains unexplained. Here, 48 Â 10 6 -atom reactive-force-field molecular dynamics simulations provide the missing link. Namely, an orderof-magnitude reduction of grain-boundary shear strength due to amorphization, combined with tensilestrength reduction, allows the crack tip to always find an easy propagation path. DOI: 10.1103/PhysRevLett.104.155502 PACS numbers: 62.20.mm, 81.05.Bx, 81.07.Bc The modification of chemical bonds due to a small amount of impurities segregated to grain boundaries (GBs) controls the mechanical properties of materials [1]. Despite decades of intense experimental [2,3] and theoretical [4][5][6] efforts, however, mechanisms of such GB mechanochemistry [7] are not well understood. In the case of sulfur (S) segregation-induced embrittlement of nickel (Ni), which is important for the development of next-generation nuclear reactors [8], Heuer et al. performed tensile tests of notched specimens with varying amount of S segregation to GBs [3]. (The maximum range of S segregation was determined to be 0.5 nm on either side of a GB.) They observed a transition from transgranular ductile fracture to intergranular brittle fracture at a critical S concentration of 15:5 AE 3:4% at GBs. In addition, they measured another critical S concentration for amorphization of Ni face-centered cubic (fcc) crystal during S þ -ion implantation [3]. The critical S concentration of 14:2 AE 3:3% for amorphization coincides with the critical S concentration for GB embrittlement within experimental error. These experiments clearly demonstrate an essential relation between amorphization and embrittlement. The central question is: What are the atomistic mechanisms that relate amorphization to embrittlement?Answering this question poses a so called multiscale simulation challenge [9], i.e., coupling quantummechanical accuracy to describe solute chemistry with large length scales to incorporate long-range stress fields and microstructures such as grains and amorphous GB phases. Recent developments in chemically reactive atomistic simulation methods and parallel computing technologies that are scalable over 10 5 processors (see [10], Fig. S1) [11], combined with those in nanomechanical experiments [12], have set the stage to address this challenge. Namely, simulations and experiments can now study the mechanical properties of nanoscale materials at the same length scale. Here, we perform large molecular dynamics (MD) simulations (see [10], Supplementary Methods) based on reactive force fields (REAXFF) [13,14], which are trained and validated (Supplementary Tables S1 and S2,[10]) by quantum-mechanical calculations based on the density functional theory [15], in order to study the effect of S segregation in nanocrystalline Ni.We first investigate the effe...

We have developed an optical system designed for detecting colored nanomaterials in aqueous solutions, using the concept of evanescent-field-coupled waveguide-mode sensors. In this study, we found that the waveguide modes induced in the sensor are intrinsically sensitive to a change in optical absorption, or a 'change in color'. The system detects less than one gold nanoparticle (diameter: 20 nm) adsorbed per square micrometer. It is also demonstrated that significant signal enhancement due to adsorption of molecules is achieved using a dye. The developed sensor rarely suffers from a drawback of impurity adsorption. The system is expected to be applied as an effective sensing tool for metal colloids, nanoparticles, and colored biomolecules in solution.

Atomically thin MoS2 layer, a promising transition metal dichalcogenide (TMDC) material, has great potential for application in next-generation electronic and optoelectronic devices. Chemical vapor deposition (CVD) is the most effective technique for the synthesis of high-quality MoS2 layers. During CVD synthesis, monolayered MoS2 is generally synthesized by sulfidation of MoO3. Although qualitative reaction mechanisms for the sulfidation of MoO3 have been investigated by previous studies, the detailed reaction processes, including atomic-scale reaction pathways and growth kinetics, have yet to be fully understood. Here, we present quantum-mechanically informed and validated reactive molecular dynamics simulations of the direct sulfidation of MoO3 surfaces using S2 gas precursors. Our work clarifies the reaction mechanisms and kinetics of the sulfidation of MoO3 surfaces as follows: the reduction and sulfidation of MoO3 surfaces occur primarily at O-termination sites, followed by unsaturated Mo sites; these local reaction processes lead to nonuniform MoO x S y surface structures during the CVD process. After annealing the MoO x S y samples, the crystallized surface structures contain voids, and three different types of local surface complexes (MoO x , MoO x S y , and MoS2-like surface regions), depending on the fraction of S ingredients on the MoO x S y surface. These results, which have been validated by our reactive quantum molecular dynamics simulations and previous experimental results, provide valuable chemical insights into the CVD synthesis of large-scale and defect-free MoS2 layers and other layered TMDC materials.

We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10(6)-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

Abstract. We occasionally encounter feline cervical or mesenteric lesions diagnosed histopathologically as abscess or inflammatory granulation tissue with eosinophil infiltration. Gram-positive cocci accompany the lesions. In the present study, such lesions obtained from 27 cats were examined to evaluate the histopathologic features and the nature of the causative bacteria. The average age was 7.3 Ϯ 3.5 years. No sex predilection was observed. Most frequent locations of the lesions included the abdominal cavity with/without mesenteric lymph nodes (11/ 27, 41%) and subcutaneous tissue or lymph nodes of the neck (9/27, 33%). Common clinical presentation was a localized mass. Grossly, the lesions contained abscesses in the center and were surrounded by fibrous tissue. Microscopically, the necrotic zone contained bacterial colonies. Large numbers of eosinophils and macrophages infiltrated the area surrounding the necrotic tissue. The surrounding connective fiber-rich granulation tissue demarcated the eosinophilic abscess. The bacteria were Gram-positive cocci in 23 of the 27 cats and were positive for anti-staphylococcus antiserum in 19 of the 23 cats. In 15 out of 17 lesions, the colonies expressed immunoreactivity to penicillin-binding protein 2Ј, which is a drug-resistance gene product of methicillin-resistant Staphylococcus (MRS) species. These findings suggest strongly that MRS causes this type of infectious lesion.