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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Crystalline metal-organic frameworks (MOFs) are formed by reticular synthesis, which creates strong bonds between inorganic and organic units. Careful selection of MOF constituents can yield crystals of ultrahigh porosity and high thermal and chemical stability. These characteristics allow the interior of MOFs to be chemically altered for use in gas separation, gas storage, and catalysis, among other applications. The precision commonly exercised in their chemical modification and the ability to expand their metrics without changing the underlying topology have not been achieved with other solids. MOFs whose chemical composition and shape of building units can be multiply varied within a particular structure already exist and may lead to materials that offer a synergistic combination of properties.

The Chemistry and Applications of Metal-Organic Frameworks

http://pubs.acs.org/doi/pdf/10.1021/cr300014x

Introduction to Metal–Organic Frameworks

We envision an autonomous sorbent materials foundry (SMF) for rapidly evaluating materials for direct air capture of carbon dioxide (CO2), specifically targeting novel metal organic framework materials. Our proposed SMF is hierarchical, simultaneously addressing the most critical gaps in the interrelated space of sorbent material synthesis, processing, properties, and performance. The ability to collect these critical data streams in an agile, coordinated, and automated fashion will enable efficient end-to-end sorbent materials design through machine-learning-driven research framework. 

Reproducible sorbent materials foundry for carbon capture at scale

Strong correlated system includes a wide class of materials that exhibit unusual electronic and magnetic properties, such as high-temperature superconductivity in copper oxides [1] and colossal magneto-resistivity in manganites [2]. YVO 3 is one such material that has at-tracted much attention due to the intricate coupling between spin, lattice, and orbital degrees of freedom. As the transition-metal ion V 3+ sits in an octahedral oxygen cage forming a perovskite structure, the correlation effects can lead to Jahn-Teller (JT) distortions, orbital ordering, charge and spin stripe formation, polaron localization, and phase separation. the and lattice dynamics in YVO 3 across its many structural and phase transitions and magnon changes 3 , information di-rect observation of the spin-waves and phonons in YVO 3

Dynamics of phase transitions in YVO3 investigated via inelastic neutron scattering and first-principles calculations

Methane storage and onboard delivery using metal-organic frameworks (MOFs) has gained significant development and realized benchmark materials with promising performance. It is still quite challenging to realize simultaneously high gravimetric...

Taner Yildirim

Papers

Reproducible sorbent materials foundry for carbon capture at scale

Dynamics of phase transitions in YVO3 investigated via inelastic neutron scattering and first-principles calculations

Promotion of methane storage capacity with metal-organic frameworks of high porosity