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

SERS Study of Co-doped TiO 2 Nanoparticles

Thermodynamics and Economics of Different Asymmetric Cold Energy Transfer in a Liquid Air Energy Storage System

MRI-based vertebral bone quality score effectively reflects bone quality in patients with osteoporotic vertebral compressive fractures

Engineered cartilage derived from mesenchymal stromal cells (MSCs) always fails to maintain the cartilaginous phenotype in the subcutaneous environment due to the ossification tendency. Vascular invasion is a prerequisite for endochondral ossification during the development of long bone. As an oral antitumor medicine, Inlyta (axitinib) possesses pronounced antiangiogenic activity, owing to the inactivation of the vascular endothelial growth factor (VEGF) signaling pathway. In this study, axitinib-loaded poly(e-caprolactone) (PCL)/collagen nanofibrous membranes are fabricated by electrospinning for the first time. Rabbit-derived MSCs-engineered cartilage is encapsulated in the axitinib-loaded nanofibrous membrane and subcutaneously implanted into nude mice. The sustained and localized release of axitinib successfully inhibits vascular invasion, stabilizes cartilaginous phenotype, and helps cartilage maturation. RNA sequence further reveals that axitinib creates an avascular, hypoxic, and low immune response niche. Timp1 is remarkably upregulated in this niche, which probably plays a functional role in inhibiting the activity of matrix metalloproteinases and stabilizing the engineered cartilage. This study provides a novel strategy for stable subcutaneous chondrogenesis of mesenchymal stromal cells, which is also suitable for other medical applications, such as arthritis treatment, local treatment of tumors, and regeneration of other avascular tissues (cornea and tendon).

https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202100351

An Avascular Niche Created by Axitinib-Loaded PCL/Collagen Nanofibrous Membrane Stabilized Subcutaneous Chondrogenesis of Mesenchymal Stromal Cells.

Defects usually have an important role in tailoring various properties of two-dimensional (2D) materials. However, optical detection of defects, especially single-atom point defects, is very challenging in 2D layers. Here, we report our systematic studies on the Raman-activated defect vibrational modes in 2D semimetallic material by combining Raman spectroscopy, density functional theory (DFT) calculation and scanning tunneling microscopy (STM). We observed three common Raman-active vibrational modes located at 95 (
 $$A_{1g}^2$$
 ), 228 (
 $$A_{1g}^1$$
 ), and 304 cm−1 (
 $$B_{1g}^1$$
 ) in ZrSiTe few-layers, consistent with our theoretical calculations. Moreover, a pronounced mode sitting at 131.7 cm−1 was found in the ZrSiTe monolayer. This mode fades out quickly in the bilayer (2L) and eventually disappears in 4L. The high-resolution STM images and DFT calculations suggest this mode to be an intralayer shear mode at the Brillouin zone boundary which is activated by atomic point defects, and STM-based inelastic tunneling spectrum further confirms the existence of such a defect mode. The appearance of such ‘forbidden’ modes in Raman spectra may pave an avenue for the optical characterization of single-atom point defects in metallic 2D layers.

/pdf/raman-detection-of-hidden-phonons-assisted-by-atomic-point-3hhvt2r9l7.pdf

Wei Ji

Papers

SERS Study of Co-doped TiO 2 Nanoparticles

Thermodynamics and Economics of Different Asymmetric Cold Energy Transfer in a Liquid Air Energy Storage System

MRI-based vertebral bone quality score effectively reflects bone quality in patients with osteoporotic vertebral compressive fractures

An Avascular Niche Created by Axitinib-Loaded PCL/Collagen Nanofibrous Membrane Stabilized Subcutaneous Chondrogenesis of Mesenchymal Stromal Cells.

Raman detection of hidden phonons assisted by atomic point defects in a two-dimensional semimetal