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

Molecular characterization and expression analyses of five genes involved in the MyD88-dependent pathway of yellow catfish (Pelteobagrus fulvidraco) responding to challenge of Aeromonas hydrophila.

STUDY DESIGN
Retrospective study.


OBJECTIVE
To evaluate the feasibility of C2 pedicle screw (C2PS) fixation with the "in-out-in" technique in patients with basilar invagination (BI).


SUMMARY OF BACKGROUND DATA
The "in-out-in" technique is a fixation technique in which the screw enters the vertebrae through the parapedicle. The technique has been used in upper cervical spine fixation. However, anatomic parameters associated with the application of this technique in patients with BI are unclear.


METHODS
We measured the C2 pedicle width (PW), the distance between vertebral artery (VA) and the transverse foramen (VATF), the safe zone and the limit zone. The lateral safe zone is the distance from the medial/lateral cortex of the C2 pedicle to the VA (LPVA/MPVA), and the medial safe zone is the distance from the medial/lateral cortex of the C2 pedicle to the dura (MPD/LPD). The lateral limit zone is the sum of LPVA/MPVA and VATF (LPTF/MPTF), and the medial limit zone is the distance from the medial/lateral cortex of the C2 pedicle to the spinal cord (MPSC/LPSC). PW, LPVA, MPVA and VATF were measured on the reconstructed CT angiography. PW, MPD, LPD, MPSC and LPSC were measured on MRI. We define a width greater than 4 mm as safe for screw. The t-test was used to compare the parameters between male and female, left and right sides in all patients, and PW in CTA and MRI data in the same patient. For intrarater reliabilities, interclass correlation coefficients were calculated.


RESULTS
A total of 154 patients (49 CTA, 143 MRI) were included. The average PW, LPVA, MPVA, LPTF, MPTF, MPD, LPD, MPSC and LPSC were 5.30 mm, 1.28 mm, 6.60 mm, 2.45 mm, 8.94 mm, 2.09 mm, 7.07 mm, 5.51 mm and 10.48 mm, respectively. Furthermore, in patients with PW ˂4 mm, 53.6% of MPVA, 86.2% of LPTF, and all limit zones were larger than 4 mm.


CONCLUSIONS
In patients with basilar invagination, there is sufficient space medially and laterally to the C2 pedicle for partial screw encroachment to achieve "in-out-in" fixation, even if the pedicle is small.


LEVEL OF EVIDENCE
4.

Feasibility of C2 Pedicle Screw Fixation with the "in-out-in" Technique for Patients with Basilar Invagination.

The quantum anomalous Hall (QAH) effect is rarely predicted in antiferromagnetic (AFM) materials. Here, by first-principles calculations, we propose that the monolayer of MoO is AFM and can be tuned to be a QAH insulator with a band gap of 50 meV. The MoO monolayer is a tetragonal lattice and we have checked its stability by the phonon spectrum and molecular dynamical simulation. It has a collinear AFM order with magnetic moments larger than $2\phantom{\rule{0.16em}{0ex}}{\ensuremath{\mu}}_{B}$ on each Mo atom. In the absence of strain, it is an AFM metal with a direct gap if spin-orbital coupling is considered. Tensile strain results in a metal-insulator phase transition, but it is still topologically trivial protected by an effective time-reversal symmetry. Shear strain breaks this symmetry and leads to the expected nontrivial electronic bands with Chern number $C=\ensuremath{-}1$. In addition, its N\'eel temperature could be larger than room temperature, providing another platform for the application of AFM materials in spintronic devices. 

Quantum anomalous Hall effect in an antiferromagnetic monolayer of MoO

The yellow catfish (Pelteobagrus fulvidraco) is an economic fish with a large breeding scale, and diseases have led to huge economic losses. Tumor necrosis factor receptor-associated factors (TRAFs) are a class of intracellular signal transduction proteins that play an important role in innate and adaptive immune responses by mediating NF-κB, JNK and MAPK signaling pathways. However, there are few studies on the TRAF gene family in yellow catfish. In this study, the open reading frame (ORF) sequences of TRAF1, TRAF2a, TRAF2b, TRAF3, TRAF4a, TRAF4b, TRAF5, TRAF6 and TRAF7 genes were cloned and identified in yellow catfish. The ORF sequences of the nine TRAF genes of yellow catfish (Pf_TRAF1-7) were 1413–2025 bp in length and encoded 470–674 amino acids. The predicted protein structures of Pf_TRAFs have typically conserved domains compared to mammals. The phylogenetic relationships showed that TRAF genes are conserved during evolution. Gene structure, motifs and syntenic analyses of TRAF genes showed that the exon–intron structure and conserved motifs of TRAF genes are diverse among seven vertebrate species, and the TRAF gene family is relatively conserved evolutionarily. Among them, TRAF1 is more closely related to TRAF2a and TRAF2b, and they may have evolved from a common ancestor. TRAF7 is quite different and distantly related to other TRAFs. Real-time quantitative PCR (qRT-PCR) results showed that all nine Pf_TRAF genes were constitutively expressed in 12 tissues of healthy yellow catfish, with higher mRNA expression levels in the gonad, spleen, brain and gill. After infection with Edwardsiella ictaluri, the expression levels of nine Pf_TRAF mRNAs were significantly changed in the head kidney, spleen, gill and brain tissues of yellow catfish, of which four genes were down-regulated and one gene was up-regulated in the head kidney; four genes were up-regulated and four genes were down-regulated in the spleen; two genes were down-regulated, one gene was up-regulated, and one gene was up-regulated and then down-regulated in the gill; one gene was up-regulated, one gene was down-regulated, and four genes were down-regulated and then up-regulated in the brain. These results indicate that Pf_TRAF genes might be involved in the immune response against bacterial infection. Subcellular localization results showed that all nine Pf_TRAFs were found localized in the cytoplasm, and Pf_TRAF2a, Pf_TRAF3 and Pf_TRAF4a could also be localized in the nucleus, uncovering that the subcellular localization of TRAF protein may be closely related to its structure and function in cellular mechanism. The results of this study suggest that the Pf_TRAF gene family plays important roles in the immune response against pathogen invasion and will provide basic information to further understand the roles of TRAF gene against bacterial infection in yellow catfish.

/pdf/molecular-characterization-of-nine-traf-genes-in-yellow-1o4dy8tl.pdf

Molecular Characterization of Nine TRAF Genes in Yellow Catfish (Pelteobagrus fulvidraco) and Their Expression Profiling in Response to Edwardsiella ictaluri Infection

Trends of miniaturized devices and quantum interference electronics lead to the long desire of Fano interference in single-molecule junctions, here, which is successfully demonstrated using the 2,7-di(4-pyridyl)-9,9'-spirobifluorene molecule with a long backbone group and a short side group. Experimentally, the two electrically coupled groups are found to contribute to two blurred degenerate points in the differential conductance mapping. This forms a characteristic non-centrosymmetric double-crossing feature, with distinct temperature response for each crossing. Theoretically, we describe the practical in-junction electron transmission using a new two-tunnelling-channel coupling model and obtain a working formula with a Fano term and a Breit-Wigner term. The formula is shown to provide a good fit for all the mapping data and their temperature dependence in three dimensions, identifying the Fano component. Our work thus forms a complete set of evidence of the Fano interference in a single-molecule junction induced by two-tunnelling-channel coupling transport. Density functional theory calculations are used to corroborate this new physics.

Wei Ji

Papers

Molecular characterization and expression analyses of five genes involved in the MyD88-dependent pathway of yellow catfish (Pelteobagrus fulvidraco) responding to challenge of Aeromonas hydrophila.

Feasibility of C2 Pedicle Screw Fixation with the "in-out-in" Technique for Patients with Basilar Invagination.

Quantum anomalous Hall effect in an antiferromagnetic monolayer of MoO

Molecular Characterization of Nine TRAF Genes in Yellow Catfish (Pelteobagrus fulvidraco) and Their Expression Profiling in Response to Edwardsiella ictaluri Infection

Fano Interference in a Single-Molecule Junction