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.

Unlike conventional materials that covalent bonds connecting atoms as the major force to hold the materials together, supramolecular biomaterials rely on noncovalent intermolecular interactions to assemble. The reversibility and biocompatibility of supramolecular biomaterials render them with diverse range of functions and lead to rapid development in the past two decades. This review focuses on the noncovalent and enzymatic control of supramolecular biomaterials, with the introduction to various triggering mechanism to initiate self-assembly. Representative applications of supramolecular biomaterials are highlighted in four categories: tissue engineering, cancer therapy, drug delivery, and molecular imaging. By introducing various applications, we intend to show enzymatic control and noncovalent interactions as a powerful tool for achieving spatiotemporal control of biomaterials both in vitro and in vivo for biomedicine.

Biomaterials based on noncovalent interactions of small molecules.

Copy number variations (CNVs) in the Neurexin 1 (NRXN1) gene, which encodes a presynaptic protein involved in neurotransmitter release, are some of the most frequently observed single-gene variants associated with autism spectrum disorder (ASD). To address the functional contribution of NRXN1 CNVs to behavioral phenotypes relevant to ASD, we carried out systematic behavioral phenotyping of an allelic series of Nrxn1 mouse models: one carrying promoter and exon 1 deletion abolishing Nrxn1α transcription, one carrying exon 9 deletion disrupting Nrxn1α protein translation, and one carrying an intronic deletion with no observable effect on Nrxn1α expression. We found that homozygous loss of Nrxn1α resulted in enhanced aggression in males, reduced affiliative social behaviors in females, and significantly altered circadian activities in both sexes. Heterozygous or homozygous loss of Nrxn1α affected the preference for social novelty in male mice, and notably, enhanced repetitive motor skills and motor coordination in both sexes. In contrast, mice bearing an intronic deletion of Nrxn1 did not display alterations in any of the behaviors assessed. These findings demonstrate the importance of Nrxn1α gene dosage in regulating social, circadian, and motor functions, and the variables of sex and genomic positioning of CNVs in the expression of autism-related phenotypes. Importantly, mice with heterozygous loss of Nrxn1, as found in numerous autistic individuals, show an elevated propensity to manifest autism-related phenotypes, supporting the use of models with this genomic architecture to study ASD etiology and assess additional genetic variants associated with autism.

/pdf/allelic-contribution-of-nrxn1a-to-autism-relevant-behavioral-3th2gd9x.pdf

Allelic contribution of Nrxn1α to autism-relevant behavioral phenotypes in mice

Chirale Metallocalix[4]arene: Trennung durch diastereomere Wolfram(IV)alkoxide

Driven by directional interparticle interactions, e.g., hydrophobic patchy, pi-pi, dipolar, and hydrogen bonding interactions, certain small molecules self-assemble in aqueous solution to form nanofibers (or other nanostructures) and consequently result in hydrogels. Because of their inherent advantages such as biocompatibility, biodegradability, and morphological resemblance of extracellular matrix (ECM), supramolecular nanofibers/hydrogels promise applications in cell culture, drug delivery, and tissue engineering. Besides the successful incorporation of bioactive molecules in the hydrogelators which perform ECM-like materials outside biological entities, it is also important to evaluate the distribution of the nanofibers in the intracellular environment and to understand their interactions with cellular components.

Supramolecular self-assembly inside living mammalian cells

As the PDT effect may be enhanced by localized hyperthermia (HT), it would be logical to find a single agent that could bring about these two modalities at precisely the target site for synergism. Since highly localized HT can be induced by magnetic field excitation of superparamagnetic nanoparticles, we report here the design and synthesis of photosensitizer-decorated iron oxide nanoparticles and their tumoricidal effect. Thus, a porphyrin is covalently anchored on the iron oxide nanoparticle via dihydroxybenzene which binds tightly on the surface of the nanoparticle by M-O bond. The morphology of the resultant nanoparticle was studied to show that the crystallinality is not changed and the nanoparticle remains superparamagnetic at room temperature. The conjugate is also strongly fluorescent indicating that the iron oxide hardly affects the optical properties of the surface bound porphyrin moieties. The conjugate is readily taken by cancer cell (Hela cell line) and is able to trigger apoptosis after excitation by light.

Bing Xu

Papers

Biomaterials based on noncovalent interactions of small molecules.

Allelic contribution of Nrxn1α to autism-relevant behavioral phenotypes in mice

Chirale Metallocalix[4]arene: Trennung durch diastereomere Wolfram(IV)alkoxide

Supramolecular self-assembly inside living mammalian cells

Photosensitizer decorated iron oxide nanoparticles : bimodal agent for combined hyperthermia and photodynamic therapy