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?

We have used the pH-induced self-assembly of a peptide-amphiphile to make a nanostructured fibrous scaffold reminiscent of extracellular matrix. The design of this peptide-amphiphile allows the nanofibers to be reversibly cross-linked to enhance or decrease their structural integrity. After cross-linking, the fibers are able to direct mineralization of hydroxyapatite to form a composite material in which the crystallographic c axes of hydroxyapatite are aligned with the long axes of the fibers. This alignment is the same as that observed between collagen fibrils and hydroxyapatite crystals in bone.

http://science.sciencemag.org/content/sci/294/5547/1684.full.pdf

Self-assembly and mineralization of peptide-amphiphile nanofibers

Supramolecular polymers can be random and entangled coils with the mechanical properties of plastics and elastomers, but with great capacity for processability, recycling, and self-healing due to their reversible monomer-to-polymer transitions. At the other extreme, supramolecular polymers can be formed by self-assembly among designed subunits to yield shape-persistent and highly ordered filaments. The use of strong and directional interactions among molecular subunits can achieve not only rich dynamic behavior but also high degrees of internal order that are not known in ordinary polymers. They can resemble, for example, the ordered and dynamic one-dimensional supramolecular assemblies of the cell cytoskeleton and possess useful biological and electronic functions.

/pdf/functional-supramolecular-polymers-3wt4hbf4y0.pdf

Functional Supramolecular Polymers

The heterogeneity of as-synthesized single-walled carbon nanotubes (SWNTs) precludes their widespread application in electronics, optics and sensing. We report on the sorting of carbon nanotubes by diameter, bandgap and electronic type using structure-discriminating surfactants to engineer subtle differences in their buoyant densities. Using the scalable technique of density-gradient ultracentrifugation, we have isolated narrow distributions of SWNTs in which >97% are within a 0.02-nm-diameter range. Furthermore, using competing mixtures of surfactants, we have produced bulk quantities of SWNTs of predominantly a single electronic type. These materials were used to fabricate thin-film electrical devices of networked SWNTs characterized by either metallic or semiconducting behaviour.

Sorting carbon nanotubes by electronic structure using density differentiation

Neural progenitor cells were encapsulated in vitro within a three-dimensional network of nanofibers formed by self-assembly of peptide amphiphile molecules. The self-assembly is triggered by mixing cell suspensions in media with dilute aqueous solutions of the molecules, and cells survive the growth of the nanofibers around them. These nanofibers were designed to present to cells the neurite-promoting laminin epitope IKVAV at nearly van der Waals density. Relative to laminin or soluble peptide, the artificial nanofiber scaffold induced very rapid differentiation of cells into neurons, while discouraging the development of astrocytes. This rapid selective differentiation is linked to the amplification of bioactive epitope presentation to cells by the nanofibers.

https://science.sciencemag.org/content/sci/303/5662/1352.full.pdf

Selective Differentiation of Neural Progenitor Cells by High-Epitope Density Nanofibers

Peptide amphiphiles are a class of molecules that combine the structural features of amphiphilic surfactants with the functions of bioactive peptides and are known to assemble into a variety of nanostructures. A specific type of peptide amphiphiles are known to self-assemble into one-dimensional nanostructures under physiological conditions, predominantly nanofibers with a cylindrical geometry. The resultant nanostructures could be highly bioactive and are of great interest in many biomedical applications, including tissue engineering, regenerative medicine, and drug delivery. In this context, we highlight our strategies for using molecular self-assembly as a toolbox to produce peptide amphiphile nanostructures and materials and efforts to translate this technology into applications as therapeutics. We also review our recent progress in using these materials for treating spinal cord injury, inducing angiogenesis, and for hard tissue regeneration and replacement.

/pdf/self-assembly-of-peptide-amphiphiles-from-molecules-to-59uxjckd9x.pdf

Samuel I. Stupp

Papers

Self-assembly and mineralization of peptide-amphiphile nanofibers

Functional Supramolecular Polymers

Sorting carbon nanotubes by electronic structure using density differentiation

Selective Differentiation of Neural Progenitor Cells by High-Epitope Density Nanofibers

Self‐assembly of peptide amphiphiles: From molecules to nanostructures to biomaterials