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

Abstract The treatment of intervertebral disc degeneration (IVDD) is still a huge challenge for clinical updated surgical techniques and basic strategies of intervertebral disc regeneration. Few studies have ever tried to combine surgery and cell therapy to bridge the gap between clinical and basic research. A prospective clinical study with a 72-month follow-up was conducted to assess the safety and feasibility of autologous discogenic cells transplantation combined with discectomy in the treatment of lumbar disc herniation (LDH) and to evaluate the regenerative ability of discogenic cells in IVDD. Forty patients with LDH who were scheduled to have discectomy enrolled in our study and were divided into the observed group (transplantation of autologous discogenic cells after discectomy) and control group (only-discectomy). Serial MRI and X-ray were used to evaluate the degenerative extent of index discs, and clinical scores were used to determine the symptomatic improvement. No adverse events were observed in the observed group, and seven patients in the control group underwent revisions. Both groups had significant improvement of all functional scores post-operatively, with the observed group improving more considerably at 36-month and 72-month follow-up. The height and water content of discs in both groups decreased significantly since 36 months post-op with the control group decreased more obviously. Discectomy combined with autologous discogenic cells transplantation is safe and feasible in the treatment of LDH. Radiological analysis demonstrated that discogenic cells transplantation could slow down the further degeneration of index discs and decrease the complications of discectomy.

Intradiscal Injection of Autologous Discogenic Cells in Patients with Discectomy: A Prospective Clinical Study of Its Safety and Feasibility

Development of critical experiments to provide validation data for multiphysics coupling codes

Providing fundamental insights in atomic interactions, dedicated methods in atomic force microscopy allow measuring the threshold forces needed to move single adsorbed atoms or molecules. However, the chemical and structural properties of the probe-tip can drastically influence the results. Establishing atomically defined contacts in such experiments, the tips in the present study are functionalized with various chemically and structurally different terminations. Xenon atoms are moved along an atomically defined metal/metal-oxide boundary where all tips show a pulling mechanism and slight force variations, which are assigned to polarization effects within the tip-sample junction. Detaching Xe atoms from the boundary involves a significantly higher energy barrier where chemical reactive Cu-tips cause Xe pickup before any lateral manipulation. Passivating the tip by inert probe particles (Xe or CO) allows further approaching the surface Xe atom. Yet, the small vertical attraction and pronounced tip relaxations prevent reaching sufficient threshold forces inducing manipulation. In contrast, the high structural rigidity of oxygen-terminated Cu-tips allows manipulations even beyond the threshold where they evolve from initial pulling, via sliding to pushing mode. The detailed quantitative analysis of the processes in the atomically defined junctions emphasizes the mechanical and chemical interactions for highly controlled experiments with piconewton sensitivity.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/smll.202101637

Mechanical and Chemical Interactions in Atomically Defined Contacts.

Multicolor imaging allows protein colocalizations and organelle interactions to be studied in biological research, which is especially important for single-molecule localization microscopy (SMLM). Here, we propose a multicolor method called excitation-resolved stochastic optical reconstruction microscopy (ExR-STORM). The method, which is based on the excitation spectrum of fluorescent dyes, successfully separated four spectrally very close far-red organic fluorophores utilizing three excitation lasers with cross-talk of less than 3%. Dyes that are only 5 nm apart in the emission spectrum were resolved, resulting in negligible chromatic aberrations. This method was extended to three-dimensional (3D) imaging by combining the astigmatic method, providing a powerful tool for resolving 3D morphologies at the nanoscale. 

/pdf/tetra-color-superresolution-microscopy-based-on-excitation-1kra9tjh.pdf

Wei Ji

Papers

Intradiscal Injection of Autologous Discogenic Cells in Patients with Discectomy: A Prospective Clinical Study of Its Safety and Feasibility

Development of critical experiments to provide validation data for multiphysics coupling codes

Mechanical and Chemical Interactions in Atomically Defined Contacts.

Tetra-color superresolution microscopy based on excitation spectral demixing

Switchable valley injection into graphene