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.

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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.

A simple visual assay based on small molecule hydrogels for detecting inhibitors of enzymes.

Small molecule hydrogels based on a class of antiinflammatory agents.

D-Glucosamine-based supramolecular hydrogels to improve wound healing

Selective inhibition of cancer cells remains a challenge in chemotherapy. Here we report the molecular and cellular validation of enzyme-instructed self-assembly (EISA) as a multiple step process for selectively killing cancer cells that overexpress alkaline phosphatases (ALPs). We design and synthesize two kinds of D-tetrapeptide containing one or two phosphotyrosine residues and with the N-terminal capped by a naphthyl group. Upon enzymatic dephosphorylation, these D-tetrapeptides turn into self-assembling molecules to form nanofibers in water. Incubating these D-tetrapeptides with several cancer cell lines and one normal cell line, the unphosphorylated D-tetrapeptides are innocuous to all the cell lines, the mono- and diphosphorylated D-tetrapeptides selectively inhibit the cancer cells, but not the normal cell. The monophosphorylated D-tetrapeptides exhibit more potent inhibitory activity than the diphosphorylated D-tetrapeptides do; the cancer cell lines express higher level of ALPs are more susceptible to inhibition by the phosphorylated D-tetrapeptides; the precursors of D-tetrapeptides that possess higher self-assembling abilities exhibit higher inhibitory activities. These results confirm the important role of enzymatic reaction and self-assembly. Using uncompetitive inhibitors of ALPs and fluorescent D-tetrapeptides, we delineate that the enzyme catalyzed dephosphorylation and the self-assembly steps, together, result in the localization of the nanofibers of D-tetrapeptides for killing the cancer cells. We find that the cell death modality likely associates with the cell type and prove the interactions between nanofibers and the death receptors. This work illustrates a paradigm-shifting and biomimetic approach and contributes useful molecular insights for the development of spatiotemporal defined supramolecular processes/assemblies as potential anticancer therapeutics.

http://pubs.acs.org/doi/pdf/10.1021/jacs.5b13541

Enzyme-Instructed Self-Assembly of Small d-Peptides as a Multiple-Step Process for Selectively Killing Cancer Cells

This feature article introduces new structural motifs (referred as "samogen") that serve as the building blocks of hydrogelators for molecular self-assembly in water to result in a series of supramolecular hydrogels. Using a compound that consists of two phenylalanine residues and a naphthyl group (also abbreviated as NapFF (1) in this text) as an example of the samogens, we demonstrated the ability of the samogens to convert bioactive molecules into molecular hydrogelators that self-assemble in water to result in nanofibers. By briefly summarizing the properties and applications (e.g., wound healing, drug delivery, controlling cell fate, typing bacteria, and catalysis) of these molecular hydrogelators derived from the samogens, we intend to illustrate the basic requirements and promises of the small-molecule hydrogelators for applications in chemistry, materials science, and biomedicine.

Bing Xu

Papers

A simple visual assay based on small molecule hydrogels for detecting inhibitors of enzymes.

Small molecule hydrogels based on a class of antiinflammatory agents.

D-Glucosamine-based supramolecular hydrogels to improve wound healing

Enzyme-Instructed Self-Assembly of Small d-Peptides as a Multiple-Step Process for Selectively Killing Cancer Cells

Versatile small-molecule motifs for self-assembly in water and the formation of biofunctional supramolecular hydrogels.