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

Thermal physical properties of the golden pomfret at low temperatures

Glutathione-responsive C2-symmetric benzene-based co-assembly hydrogels.

Twenty-three polymorphic microsatellite loci were isolated from Schizothorax macropogon and were characterized in 42 individuals collected from the Yarlung Tsangpo River in Tibet, China The number of alleles per locus ranged from 5 to 32 with an average of 2017 The expected heterozygosity and Shannon-Wiener diversity index ranged from 0709 to 0951 and from 1421 to 3183, respectively These microsatellite loci will be valuable for the evaluation of genetic diversity and population genetic structure of S macropogon

Isolation and characterization of twenty-three polymorphic microsatellite loci in Schizothorax macropogon

Electrochemical surface-enhanced Raman scattering (EC-SERS) spectroscopy is an ultrasensitive spectro-electrochemistry technique that provides mechanistic and dynamic information on electrochemical interfaces at the molecular level. However, the plasmon-mediated photocatalysis hinders the intrinsic electrochemical behavior of molecules at electrochemical interfaces. This work aimed to develop a facile method for constructing a reliable EC-SERS substrate that can be used to study the molecular dynamics at electrochemical interfaces. Herein, a novel Ag-WO3−x electrochromic heterostructure was synthesized for EC-SERS. Especially, the use of electrochromic WO3−x film suppresses the influence of hot-electrons-induced catalysis while offering a reliable SERS effect. Based on this finding, the real electrochemical behavior of p-aminothiophenol (PATP) on Ag nanoparticles (NPs) surface was revealed for the first time. We are confident that metal-semiconductor electrochromic heterostructures could be developed into reliable substrates for EC-SERS analysis. Furthermore, the results obtained in this work provide new insights not only into the chemical mechanism of SERS, but also into the hot-electron transfer mechanism in metal-semiconductor heterostructures.

/pdf/an-electrochromic-ag-decorated-wo3-x-film-with-adjustable-3sf7clpf.pdf

An Electrochromic Ag-Decorated WO3−x Film with Adjustable Defect States for Electrochemical Surface-Enhanced Raman Spectroscopy

When modeling a neutron transport process, the probabilities of neutron interactions with target materials must be accounted for properly. These interaction probabilities, or cross sections, are strong functions of the neutron energy and the target material temperature. We usually pre-calculate and store cross sections at many energies and temperatures to be used in neutron transport codes. For problems involving a coupling of neutronics and thermal hydraulics, pre-storing cross sections becomes memory intensive because of the fine temperature mesh needed to account for temperature feedback. For Very High Temperature Reactors (VHTR), many cross sections are needed on a fine temperature mesh to resolve the TRISO particle fuel and to account for high temperatures during accident scenarios like the Loss of Forced Cooling (LOFC) [1]. Methods have been developed in recent years to reduce cross section data storage in the resolvedresonance and epithermal energy ranges by generating the temperature-dependent cross sections on-the-fly [2,3]. In these on-the-fly methodologies, the energy distribution of the target nuclide is assumed to follow a MaxwellBoltzmann distribution, allowing for analytical expressions to be formed to drive the on-the-fly process. At thermal neutron energies, however, this assumption is not valid as chemical binding effects are dominant which complicates the calculation of the differential scattering cross section. A new strategy is needed to treat the temperature dependence of the double differential scattering data in the thermal energy region. This paper presents an on-thefly strategy to sample a neutron’s outgoing energy and scattering angle after a thermal scattering event for an arbitrary temperature. A method proposed by Ballinger [4] is introduced to construct probability density functions (PDFs) of momentum transfer (α) and energy transfer (β). The cumulative distribution functions (CDFs) of these PDFs are then constructed on a temperature mesh and an incoming energy mesh for common moderator nuclei. Regression models are then used to fit the temperature dependence of these CDFs. The best functional fits are chosen based on an error analysis procedure and the outgoing parameters are then sampled on-the-fly from the coefficients of the chosen functional fits. MOTIVATION

http://neams.rpi.edu/jiw2/papers/ANS%20110%20Pavlou.pdf

Wei Ji

Papers

Thermal physical properties of the golden pomfret at low temperatures

Glutathione-responsive C2-symmetric benzene-based co-assembly hydrogels.

Isolation and characterization of twenty-three polymorphic microsatellite loci in Schizothorax macropogon

An Electrochromic Ag-Decorated WO3−x Film with Adjustable Defect States for Electrochemical Surface-Enhanced Raman Spectroscopy

A Temperature Dependence Study of Alpha/Beta Cumulative Distribution Functions Based on S(α,β) Data