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

A critical review of the emerging field of MOF-based catalysis is presented. Discussed are examples of: (a) opportunistic catalysis with metal nodes, (b) designed catalysis with framework nodes, (c) catalysis by homogeneous catalysts incorporated as framework struts, (d) catalysis by MOF-encapsulated molecular species, (e) catalysis by metal-free organic struts or cavity modifiers, and (f) catalysis by MOF-encapsulated clusters (66 references).

Metal–organic framework materials as catalysts

비만아 부모의 돌봄 경험: q 방법론

Provided, inter alia, are synthetic melanin nanoparticles (MelNPs) useful for protecting keratinocytes from UV-damage and for treating melanin-defective diseases.

Synthetic melanin nanoparticles uses thereof

The surface charge densities, apparent equilibrium binding constants, and free energies of binding of nickel ions to supported and suspended lipid membranes prepared from POPC and two types of lipopolysaccharide (LPS) are reported. Second- and third-order nonlinear optical mixing shows that rough LPS (rLPS)-incorporated bilayers carry the highest charge density and provide the most binding sites for nickel ions while LPS-free bilayers exhibit the lowest charge density and fewest binding sites. Ni2+ binding is almost fully reversible at low concentrations but less so at higher Ni2+ concentrations. Ni2+ adsorption isotherms exhibit hysteresis loops. The role of interfacial depth on the observed second harmonic generation (SHG) responses is discussed in the context of complementary dynamic light scattering, X-ray spectroscopy, and cryogenic transmission electron microscopy experiments. The latter reveal considerable Ni2+-induced structural deformations to the bacterial membrane models containing the short, O-antigen-free rLPS, consistent with complex formation on the vesicle surfaces that involve Ni2+ ions and carboxylate groups in the inner core of rLPS. In contrast, Ni2+ ion complexation to the charged groups (phosphates and carboxylate) of the considerably longer O-antigen units in sLPS appears to protect the phospholipid backbone against metal binding and thus preserve the vesicle structure.

Bacterial Model Membranes Deform (resp. Persist) upon Ni2+ Binding to Inner Core (resp. O-Antigen) of Lipopolysaccharides

Stimuli-responsive nanoparticles, when injected systemically, circulate in the blood stream until reaching the site of myocardial infarction (MI). As reported by N. C. Gianneschi, K. L. Christman, and co-workers on page 5547, recognition by infarct-associated enzymes induces a morphology transition, triggering the subsequent aggregation of nanoparticles at the site of damage. The resulting microscale aggregates exhibit prolonged retention in the infarct, thereby providing a potential platform for delivering therapeutics to an acute MI.

Stimuli‐Responsive Materials: Enzyme‐Responsive Nanoparticles for Targeted Accumulation and Prolonged Retention in Heart Tissue after Myocardial Infarction (Adv. Mater. 37/2015)

We describe a composite in which reactive hexa-nuclear zirconium (Zr6) clusters were encapsulated in the micropores of processable polymers of intrinsic microporosity (PIMs). By varying the amount of Zr6 clusters in PIMs, it was possible to tune the loading of Zr6 in two polymer matrices: the pristine PIM-1 and the amidoxime-functionalized PIM (PIM-1-AO). Aggregation of Zr6 clusters was suppressed in both Zr6@PIM composites to achieve improved hydrolysis performance of a nerve agent simulant, dimethyl 4-nitrophenylphosphate (DMNP). Low-loading Zr6@PIM-1-AO was found to be the best catalyst, with a DMNP hydrolysis half-life of less than 1 h, which is comparable to some zirconium metal–organic frameworks (Zr-MOFs) at higher catalyst loading. Further, these composites can be electrospun into reactive nanofibers. This demonstrates a new route to apply porous polymers as matrices to encapsulate, stabilize, and utilize the reactivity of soluble Zr6 clusters, which could act as effective candidate materials for the fabrication of personal protective equipment (PPE) against nerve agents. 

Aggregation-Suppressed Porous Processable Hexa-Zirconium/Polymer Composites for Detoxification of a Nerve Agent Simulant

Allomelanin is a class of nitrogen-free melanin mostly found in fungi and, like all naturally occurring melanins, is hydrophilic. Herein, we develop a facile method to modify synthetic hydrophilic allomelanin to yield hydrophobic derivatives through post-synthetic modifications. Amine-functionalized molecules of various kinds can be conjugated to allomelanin nanoparticles under mild conditions with high loading efficiencies. Hydrophobicity is conferred by introducing amine-terminated alkyl groups with different chain lengths. We demonstrate that the resulting hydrophobic allomelanin nanoparticles undergo air/water interfacial self-assembly in a controlled fashion, which enables the generation of large-scale and uniform structural colors. This work provides an efficient and tunable surface chemistry modification strategy to broaden the scope of synthetic melanin structure and function beyond the known diversity found in nature. 

https://biblio.ugent.be/publication/01GRK3XD4ZY75YM2TQ57TH64N6/file/01GRK3ZPKWX0VDMAAFDWGE6MT9.pdf

Nathan C. Gianneschi

Papers

Synthetic melanin nanoparticles uses thereof

Bacterial Model Membranes Deform (resp. Persist) upon Ni2+ Binding to Inner Core (resp. O-Antigen) of Lipopolysaccharides

Stimuli‐Responsive Materials: Enzyme‐Responsive Nanoparticles for Targeted Accumulation and Prolonged Retention in Heart Tissue after Myocardial Infarction (Adv. Mater. 37/2015)

Aggregation-Suppressed Porous Processable Hexa-Zirconium/Polymer Composites for Detoxification of a Nerve Agent Simulant

Hydrophobic Melanin via Post-Synthetic Modification for Controlled Self-Assembly