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

Self-assembly is the autonomous organization of components into patterns or structures without human intervention. Self-assembling processes are common throughout nature and technology. They involve components from the molecular (crystals) to the planetary (weather systems) scale and many different kinds of interactions. The concept of self-assembly is used increasingly in many disciplines, with a different flavor and emphasis in each.

http://science.sciencemag.org/content/sci/295/5564/2418.full.pdf

Self-assembly at all scales.

A family of highly ordered mesoporous (20−300 A) silica structures have been synthesized by the use of commercially available nonionic alkyl poly(ethylene oxide) (PEO) oligomeric surfactants and poly(alkylene oxide) block copolymers in acid media. Periodic arrangements of mescoscopically ordered pores with cubic Im3m, cubic Pm3m (or others), 3-d hexagonal (P63/mmc), 2-d hexagonal (p6mm), and lamellar (Lα) symmetries have been prepared. Under acidic conditions at room temperature, the nonionic oligomeric surfactants frequently form cubic or 3-d hexagonal mesoporous silica structures, while the nonionic triblock copolymers tend to form hexagonal (p6mm) mesoporous silica structures. A cubic mesoporous silica structure (SBA-11) with Pm3m diffraction symmetry has been synthesized in the presence of C16H33(OCH2CH2)10OH (C16EO10) surfactant species, while a 3-d hexagonal (P63/mmc) mesoporous silica structure (SBA-12) results when C18EO10 is used. Surfactants with short EO segments tend to form lamellar mesost...

Nonionic Triblock and Star Diblock Copolymer and Oligomeric Surfactant Syntheses of Highly Ordered, Hydrothermally Stable, Mesoporous Silica Structures

As a fascinating conjugated polymer, graphitic carbon nitride (g-C3N4) has become a new research hotspot and drawn broad interdisciplinary attention as a metal-free and visible-light-responsive photocatalyst in the arena of solar energy conversion and environmental remediation. This is due to its appealing electronic band structure, high physicochemical stability, and “earth-abundant” nature. This critical review summarizes a panorama of the latest progress related to the design and construction of pristine g-C3N4 and g-C3N4-based nanocomposites, including (1) nanoarchitecture design of bare g-C3N4, such as hard and soft templating approaches, supramolecular preorganization assembly, exfoliation, and template-free synthesis routes, (2) functionalization of g-C3N4 at an atomic level (elemental doping) and molecular level (copolymerization), and (3) modification of g-C3N4 with well-matched energy levels of another semiconductor or a metal as a cocatalyst to form heterojunction nanostructures. The constructi...

Graphitic Carbon Nitride (g-C3N4)-Based Photocatalysts for Artificial Photosynthesis and Environmental Remediation: Are We a Step Closer To Achieving Sustainability?

This paper presents results on controlling the surface morphology of evaporation-driven self-assembly of peptide amphiphile (PA) nanofibers by dip-pen nanolithography. These PA nanofibers, which measure only a few nanometers in diameter, can be oriented perpendicularly to the receding edge of a solution. Dragging a meniscus of PA ink with an atomic force microscope (AFM) tip creates reproducibly aligned arrays of isolated and close-packed PA nanofiber patterns on silicon substrates, utilizing surface coating of poly(ethylene glycol) to suppress the self-assembly of nanofibers on AFM tips. We also demonstrate the ability to construct double-layer patterns of differing nanofiber orientations at the same position. This result could be important in producing a complex, multilayer pattern of these peptide-based supramolecular nanostructures.

Dip-pen patterning and surface assembly of peptide amphiphiles.

https://www.tpbin.com/Uploads/Subjects/5f1111cf-1a57-4d8c-ab38-efbf71b1dd99.pdf

Mineralization of peptide amphiphile nanofibers and its effect on the differentiation of human mesenchymal stem cells.

A composition and method for repairing damaged connective tissue is provided. The composition comprises pseudo-poly(amino acids) and/or classic poly(amino acids) that exhibit adhesiveness for connective tissues. The composition is formed into an adhesive tissue repair implant and pressed against the damaged tissue to adhere the adhesive composition to the tissue.

Poly(amino acid) adhesive tissue grafts

Amphiphilic molecules can form closed-shell structures that are determined by competing attractive and repulsive forces. Since supramolecular shape has its roots in intermolecular interactions, the interplay of electrostatic, hydrophobic, and steric forces can generate nonspherical structures. Here we show that anionic and cationic amphiphiles of unequal charge can coassemble into small buckled vesicles and present a physical argument that explains this phenomenon. The strong electrostatic interaction between the +3 and -1 head groups increases the cohesion energy of the amphiphiles and favors the formation of two-dimensional, flat ionic domains on the vesicle surface, resulting in edges and a buckled shape.

/pdf/buckled-membranes-in-mixed-valence-ionic-amphiphile-vesicles-2rrzyzfvh8.pdf

Buckled Membranes in Mixed-Valence Ionic Amphiphile Vesicles Analyzed by X-Ray Scattering

Astrogliosis with glial scar formation after damage to the nervous system is a major impediment to axonal regeneration and functional recovery. The present study examined the role of β1-integrin signaling in regulating astrocytic differentiation of neural stem cells. In the adult spinal cord β1-integrin is expressed predominantly in the ependymal region where ependymal stem cells (ESCs) reside. β1-integrin signaling suppressed astrocytic differentiation of both cultured ESCs and subventricular zone (SVZ) progenitor cells. Conditional knockout of β1-integrin enhanced astrogliogenesis both by cultured ESCs and by SVZ progenitor cells. Previous studies have shown that injection into the injured spinal cord of a self-assembling peptide amphiphile that displays an IKVAV epitope (IKVAV-PA) limits glial scar formation and enhances functional recovery. Here we find that injection of IKVAV-PA induced high levels of β1-integrin in ESCs in vivo, and that conditional knockout of β1-integrin abolished the astroglial suppressive effects of IKVAV-PA in vitro. Injection into an injured spinal cord of PAs expressing two other epitopes known to interact with β1-integrin, a Tenascin C epitope and the fibronectin epitope RGD, improved functional recovery comparable to the effects of IKVAV-PA. Finally we found that the effects of β1-integrin signaling on astrogliosis are mediated by integrin linked kinase (ILK). These observations demonstrate an important role for β1-integrin/ILK signaling in regulating astrogliosis from ESCs and suggest ILK as a potential target for limiting glial scar formation after nervous system injury.

/pdf/b1-integrin-and-integrin-linked-kinase-regulate-astrocytic-1qsjezbj0s.pdf

Samuel I. Stupp

Papers

Dip-pen patterning and surface assembly of peptide amphiphiles.

Mineralization of peptide amphiphile nanofibers and its effect on the differentiation of human mesenchymal stem cells.

Poly(amino acid) adhesive tissue grafts

Buckled Membranes in Mixed-Valence Ionic Amphiphile Vesicles Analyzed by X-Ray Scattering

β1-Integrin and integrin linked kinase regulate astrocytic differentiation of neural stem cells.