Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

BACKGROUND Materials by design is an appealing idea that is very hard to realize in practice. Combining the best of different ingredients in one ultimate material is a task for which we currently have no general solution. However, we do have some successful examples to draw upon: Composite materials and III-V heterostructures have revolutionized many aspects of our lives. Still, we need a general strategy to solve the problem of mixing and matching crystals with different properties, creating combinations with predetermined attributes and functionalities. ADVANCES Two-dimensional (2D) materials offer a platform that allows creation of heterostructures with a variety of properties. One-atom-thick crystals now comprise a large family of these materials, collectively covering a very broad range of properties. The first material to be included was graphene, a zero-overlap semimetal. The family of 2D crystals has grown to includes metals (e.g., NbSe 2 ), semiconductors (e.g., MoS 2 ), and insulators [e.g., hexagonal boron nitride (hBN)]. Many of these materials are stable at ambient conditions, and we have come up with strategies for handling those that are not. Surprisingly, the properties of such 2D materials are often very different from those of their 3D counterparts. Furthermore, even the study of familiar phenomena (like superconductivity or ferromagnetism) in the 2D case, where there is no long-range order, raises many thought-provoking questions. A plethora of opportunities appear when we start to combine several 2D crystals in one vertical stack. Held together by van der Waals forces (the same forces that hold layered materials together), such heterostructures allow a far greater number of combinations than any traditional growth method. As the family of 2D crystals is expanding day by day, so too is the complexity of the heterostructures that could be created with atomic precision. When stacking different crystals together, the synergetic effects become very important. In the first-order approximation, charge redistribution might occur between the neighboring (and even more distant) crystals in the stack. Neighboring crystals can also induce structural changes in each other. Furthermore, such changes can be controlled by adjusting the relative orientation between the individual elements. Such heterostructures have already led to the observation of numerous exciting physical phenomena. Thus, spectrum reconstruction in graphene interacting with hBN allowed several groups to study the Hofstadter butterfly effect and topological currents in such a system. The possibility of positioning crystals in very close (but controlled) proximity to one another allows for the study of tunneling and drag effects. The use of semiconducting monolayers leads to the creation of optically active heterostructures. The extended range of functionalities of such heterostructures yields a range of possible applications. Now the highest-mobility graphene transistors are achieved by encapsulating graphene with hBN. Photovoltaic and light-emitting devices have been demonstrated by combining optically active semiconducting layers and graphene as transparent electrodes. OUTLOOK Currently, most 2D heterostructures are composed by direct stacking of individual monolayer flakes of different materials. Although this method allows ultimate flexibility, it is slow and cumbersome. Thus, techniques involving transfer of large-area crystals grown by chemical vapor deposition (CVD), direct growth of heterostructures by CVD or physical epitaxy, or one-step growth in solution are being developed. Currently, we are at the same level as we were with graphene 10 years ago: plenty of interesting science and unclear prospects for mass production. Given the fast progress of graphene technology over the past few years, we can expect similar advances in the production of the heterostructures, making the science and applications more achievable.

2D materials and van der Waals heterostructures

The natural high brittleness of sapphire leads to its poor machinability, which limits its application shape and size. The connection between sapphire and metal provides a new method to prepare large-size sapphire components and complex structural parts. In this study, sapphire and TC4 alloy were joined by spark plasma sintering (SPS) diffusion technology with Al2O3-Ti as interlayer fillers. The effects of filler composition, sintering temperature, microstructure, and phase distribution on the strength of the joint were explored. The results showed that sapphire and TC4 could be well connected by SPS with Al2O3-Ti fillers. The microstructure of the joint showed no obvious defect or element enrichment. The optimized shear strength of sapphire/interlayer(Al2O3-Ti)/TC4 joint reached 121 MPa, and the fracture path mode was sapphire-interlayer-TC4, indicating the strong bonding between the heterogeneous materials. The sapphire/interlayer(Al2O3-Ti)/TC4 structure could relieve the residual stress caused by the difference in the thermal expansion coefficient in direct connection between sapphire and TC4. 

Heterogeneous material joining of sapphire and TC4 alloy with a functionally graded interface

Background: Dendrobium nobile (D. nobile), a traditional Chinese medicine, has received attention as an anti-tumor drug, but its mechanism is still unclear. In this study, we applied network pharmacology, bioinformatics, and in vitro experiments to explore the effect and mechanism of Dendrobin A, the active ingredient of D. nobile, against pancreatic ductal adenocarcinoma (PDAC). Methods: The databases of SwissTargetPrediction and PharmMapper were used to obtain the potential targets of Dendrobin A, and the differentially expressed genes (DEGs) between PDAC and normal pancreatic tissues were obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases. The protein-protein interaction (PPI) network for Dendrobin A anti-PDAC targets was constructed based on the STRING database. Molecular docking was used to assess Dendrobin A anti-PDAC targets. PLAU, one of the key targets of Dendrobin A anti-PDAC, was immunohistochemically stained in clinical tissue arrays. Finally, in vitro experiments were used to validate the effects of Dendrobin A on PLAU expression and the proliferation, apoptosis, cell cycle, migration, and invasion of PDAC cells. Results: A total of 90 genes for Dendrobin A anti-PDAC were screened, and a PPI network for Dendrobin A anti-PDAC targets was constructed. Notably, a scale-free module with 19 genes in the PPI indicated that the PPI is highly credible. Among these 19 genes, PLAU was positively correlated with the cachexia status while negatively correlated with the overall survival of PDAC patients. Through molecular docking, Dendrobin A was found to bind to PLAU, and the Dendrobin A treatment led to an attenuated PLAU expression in PDAC cells. Based on clinical tissue arrays, PLAU protein was highly expressed in PDAC cells compared to normal controls, and PLAU protein levels were associated with the differentiation and lymph node metastatic status of PDAC. In vitro experiments further showed that Dendrobin A treatment significantly inhibited the proliferation, migration, and invasion, inducing apoptosis and arresting the cell cycle of PDAC cells at the G2/M phase. Conclusion: Dendrobin A, a representative active ingredient of D. nobile, can effectively fight against PDAC by targeting PLAU. Our results provide the foundation for future PDAC treatment based on D. nobile.

/pdf/integrated-analysis-of-dendrobium-nobile-extract-dendrobin-a-2zhbaqfk.pdf

Integrated analysis of Dendrobium nobile extract Dendrobin A against pancreatic ductal adenocarcinoma based on network pharmacology, bioinformatics, and validation experiments

Topology and ferrovalley (FV) are two essential concepts in emerging device applications and the fundamental research field. To date, relevant reports are extremely rare about the coupling of FV and topology in a single system. By Monte Carlo (MC) simulations and first-principles calculations, a stable intrinsic FV ScBrI semiconductor with high Curie temperature (TC) is predicted. Because of the combination of spin-orbital coupling (SOC) and exchange interaction, the Janus monolayer ScBrI shows a spontaneous valley polarization of 90 meV, which is located in the top valence band. For the magnetization direction perpendicular to the plane, the changes from FV to half-valley-metal (HVM), to valley-nonequilibrium quantum anomalous Hall effect (VQAHE), to HVM, and to FV can be induced by strain engineering. It is worth noting that there are no particular valley polarization and VQAHE states for in-plane (IP) magnetic anisotropy. By obtaining the real magnetic anisotropy energy (MAE) under different strains, due to spontaneous valley polarization, intrinsic out-of-plane (OOP) magnetic anisotropy, a chiral edge state, and a unit Chern number, the VQAHE can reliably appear between two HVM states. The increasing strains can induce VQAHE, which can be clarified by a band inversion between dx2-y2/dxy and dz2 orbitals, and a sign-reversible Berry curvature. Once synthesized, the Janus monolayer ScBrI would find more significant applications in topological electronic, valleytronic, and spintronic nanodevices.

Spontaneous valley polarization and valley-nonequilibrium quantum anomalous Hall effect in Janus monolayer ScBrI.

https://www.onlinelibrary.wiley.com/doi/epdf/10.1002/anie.201910159

Inside Back Cover: Enhanced Raman Scattering by ZnO Superstructures: Synergistic Effect of Charge Transfer and Mie Resonances (Angew. Chem. Int. Ed. 41/2019)

The DOE NEAMS Workbench project is creating a unified interface for multi-fidelity and multi-physics simulations incorporating a suite of nuclear engineering codes [1]. Through its unified interface, Workbench will make its constituent codes easier to use and more powerful by increasing connectivity between codes. A fundamental part of connecting these codes is model unification. For the different codes to work together, they need to be operating on the same model (geometry, boundary conditions, etc.). To obtain the most accurate results, each code should be using the exact same model rather than trying to reproduce the same model with each code’s own modelling tools. Using each code’s own modeling tools will produce models that clearly reflect the same physical system, but it is unlikely that the models will be precisely the same. Consider MCNP6.2 and PROTEUS, two reactor physics codes being integrated into Workbench [2, 3, 4]. Even though both codes perform reactor physics simulations, their models are defined quite differently. PROTEUS requires an unstructured mesh to define its geometry while MCNP6.2 relies on constructive solid geometry (CSG). Both of these methods are valid ways to represent the underlying physical system, but will produce slightly different geometries. These geometric variations are usually minimal, but still will cause volumetric differences between the two models. Even with only small changes in volume the results for sensitive applications, such as criticality, can notably change. This issue can be circumvented by utilizing MCNP6.2’s unstructured mesh capabilities. MCNP6.2 can generate its CSG model based on an unstructured mesh [5]. Using this feature, an unstructured mesh for PROTEUS can also be used for MCNP6.2. This makes it possible to create a unified model for both codes since MCNP6.2’s geometry will also be derived from the unstructured mesh (just like with PROTEUS). With a unified model, using MCNP6.2 as a benchmark for PROTEUS problems becomes more accurate since differences in simulation results from geometry discrepancies can be ruled out. An additional benefit is that any models already created for PROTEUS can be used by MCNP6.2 as well. This provides a MCNP6.2 user with a variety of ready to use reactor models. While MCNP6.2 can in principle use an unstructured mesh from PROTEUS, a PROTEUS mesh cannot be directly loaded into MCNP6.2. This is because each code is restricted to a specific mesh file format. Fig. 1 shows the general unstructured mesh workflows for PROTEUS and MCNP6.2. It can clearly be seen that these are entirely separate processes starting from the different meshing programs, Abaqus and Cubit. Fig. 1. Standard Unstructured Mesh Workflows.

Wei Ji

Papers

Heterogeneous material joining of sapphire and TC4 alloy with a functionally graded interface

Integrated analysis of Dendrobium nobile extract Dendrobin A against pancreatic ductal adenocarcinoma based on network pharmacology, bioinformatics, and validation experiments

Spontaneous valley polarization and valley-nonequilibrium quantum anomalous Hall effect in Janus monolayer ScBrI.

Inside Back Cover: Enhanced Raman Scattering by ZnO Superstructures: Synergistic Effect of Charge Transfer and Mie Resonances (Angew. Chem. Int. Ed. 41/2019)

Unstructured Mesh Unification for MCNP6.2 and PROTEUS in NEAMS Workbench