There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

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

We report a method to form multifunctional polymer coatings through simple dip-coating of objects in an aqueous solution of dopamine. Inspired by the composition of adhesive proteins in mussels, we used dopamine self-polymerization to form thin, surface-adherent polydopamine films onto a wide range of inorganic and organic materials, including noble metals, oxides, polymers, semiconductors, and ceramics. Secondary reactions can be used to create a variety of ad-layers, including self-assembled monolayers through deposition of long-chain molecular building blocks, metal films by electroless metallization, and bioinert and bioactive surfaces via grafting of macromolecules.

/pdf/mussel-inspired-surface-chemistry-for-multifunctional-1noq7vcby7.pdf

Mussel-Inspired Surface Chemistry for Multifunctional Coatings

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

Synthesis and antibacterial activities of multivalent vancomycins based on 8-hydroxyquinoline platforms

Here we report the synthesis and effect on the cell viability of pyrrole-conjugated phosphopeptides. Encouraged by the selective inhibition of cancer cells by a naphthyl-capped phosphopeptide (Nap-ffpy, 1), we conjugated the heteroaromatic dipyrrole or tripyrrole motif at the N-terminal of short peptides containing phosphotyrosine or phosphoserine and examined the bioactivity of the resulting phosphopeptides (2–10). Although most of the phosphopeptides exhibit comparable activities with that of 1 against HeLa cells at 200 μM, they, differing from 1, are largely compatible with HeLa cells at 400 μM. Enzymatic dephosphorylation of 2–10, at 400 μM is unable to induce a dramatic morphological transition of the peptide assemblies observed in the case of 1. These results suggest that a heteroaromatic motif at the N-terminal of peptides likely disfavors the formation of extensive nanofibers or morphological changes during enzymatic self-assembly, thus provide useful insights for the development of phosphopeptides as substrates of phosphatases for controlling cell fate.

/pdf/synthesis-and-bioactivity-of-pyrrole-conjugated-188ansfq.pdf

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

/pdf/instructed-assembly-as-context-dependent-nanoscale-signals-61hrbo10a4.pdf

Instructed-Assembly as Context-Dependent Nanoscale Signals for Death and Morphogenesis of Cells

A new anionic porphyrin-phosphate conjugate has been made as the substrate of phosphatase to evaluate its cellular-uptake
and potential targeting on cancer cells, taking advantage of the over-expression of phosphatases associated with
the development of cancers. The phosphate groups increase the hydrophilicity of porphyrin dityrosine phosphate and
facilitate its formulation in aqueous solvent. Upon hydrolysis by phosphatase after cellular uptaking, the more
hydrophobic porphyrin-dityrosine promises to give better cellular retention. Indeed, the phosphate conjugate displayed a
much better PDT effect than that of the parent porphyrin at the same concentration (10 mM) and light dosage on HeLa
cells, indicating the enzyme-cleavage reaction occurred in HeLa cells plays a role. Photosenzitizers utilizing enzyme-cleavage
might be a promising approach for photodynamic therapy.

Bing Xu

Papers

Synthesis and antibacterial activities of multivalent vancomycins based on 8-hydroxyquinoline platforms

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

Instructed-Assembly as Context-Dependent Nanoscale Signals for Death and Morphogenesis of Cells

Enhancing PDT drug delivery by enzymatic cleavage of porphyrin phosphates

Design and synthesis of coordination polymer gels