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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

비만아 부모의 돌봄 경험: q 방법론

Block copolymer (BCP) self-assembly has attracted considerable attention for many decades because it can yield ordered structures in a wide range of morphologies, including spheres, cylinders, bicontinuous structures, lamellae, vesicles, and many other complex or hierarchical assemblies. These aggregates provide potential or practical applications in many fields. The present tutorial review introduces the primary principles of BCP self-assembly in bulk and in solution, by describing experiments, theories, accessible morphologies and morphological transitions, factors affecting the morphology, thermodynamics and kinetics, among others. As one specific example at a more advanced level, BCP vesicles (polymersomes) and their potential applications are discussed in some detail.

/pdf/self-assembly-of-block-copolymers-381hzqnmce.pdf

Self-assembly of block copolymers

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

By combining three mutually immiscible polymeric components in a mixed-arm star block terpolymer architecture, we have observed the formation of a previously unknown class of multicompartment micelles in dilute aqueous solution. Connection of water-soluble poly(ethylene oxide) and two hydrophobic but immiscible components (a polymeric hydrocarbon and a perfluorinated polyether) at a common junction leads to molecular frustration when dispersed in aqueous solution. The incompatible hydrophobic blocks form cores that are protected from the water by the poly(ethylene oxide) blocks, but both are forced to make contact with the poly(ethylene oxide) by virtue of the chain architecture. The structures that emerge depend on the relative lengths of the blocks and can be tuned from discrete multicompartment micelles to extended wormlike structures with segmented cores.

https://science.sciencemag.org/content/sci/306/5693/98.full.pdf

Multicompartment micelles from ABC miktoarm stars in water.

Four amphiphilic poly((1,2-butadiene)-block-ethylene oxide) (PB−PEO) diblock copolymers were shown to aggregate strongly and form micelles in an ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]). The universal micellar structures (spherical micelle, wormlike micelle, and bilayered vesicle) were all accessed by varying the length of the corona block while holding the core block constant. The nanostructures of the PB−PEO micelles formed in an ionic liquid were directly visualized by cryogenic transmission electron microscopy (cryo-TEM). Detailed micelle structural information was extracted from both cryo-TEM and dynamic light scattering measurements, with excellent agreement between the two techniques. Compared to aqueous solutions of the same copolymers, [BMIM][PF6] solutions exhibit some distinct features, such as temperature-independent micellar morphologies between 25 and 100 °C. As in aqueous solutions, significant nonergodicity effects were also observed. This work demonstrat...

Self-assembly of block copolymer micelles in an ionic liquid

A rapidly formed supramolecular polypeptide-DNA hydrogel was prepared and used for in situ multilayer three-dimensional bioprinting for the first time. By alternative deposition of two complementary bio-inks, designed structures can be printed. Based on their healing properties and high mechanical strengths, the printed structures are geometrically uniform without boundaries and can keep their shapes up to the millimeter scale without collapse. 3D cell printing was demonstrated to fabricate live-cell-containing structures with normal cellular functions. Together with the unique properties of biocompatibility, permeability, and biodegradability, the hydrogel becomes an ideal biomaterial for 3D bioprinting to produce designable 3D constructs for applications in tissue engineering.

/pdf/rapid-formation-of-a-supramolecular-polypeptide-dna-hydrogel-1wdimoc5ep.pdf

Rapid formation of a supramolecular polypeptide-DNA Hydrogel for in situ three-dimensional multilayer bioprinting

The stimuli-responsive polypeptides have drawn extensive attention because of their promising applications in biotechnology considering their biocompatibility, biodegradability, and bioactivity In this tutorial review, we summarize the most recent progress in this area, including thermo-, redox-, photo-, and biomolecule responsive polypeptides over the past decade The design and synthesis of stimuli-responsive polypeptides will be briefly introduced The correlation between the structure and properties, particularly the effects of polypeptide conformation, will be emphasized here In addition, the applications of stimuli-responsive polypeptides in controlled drug release and tissue engineering are briefly discussed

Biodegradable stimuli-responsive polypeptide materials prepared by ring opening polymerization

Several new multicompartment micellar structures have been identified by cryogenic transmission electron microscopy (cryoTEM) from the aqueous self-assembly of mu-[poly(ethylethylene)][poly(ethylene oxide)][poly(perfluoropropylene oxide)] (mu-EOF) miktoarm star terpolymers. This work extends our previous studies, in which it was found that, upon decreasing the length of the hydrophilic block (O), the resulting micelles evolved from "hamburger" micelles to segmented worms and ultimately to nanostructured bilayers and vesicles. In the terpolymers examined here segmented ribbons and bilayers were found at an intermediate composition between segmented worms and nanostructured bilayers, provided that the fluoropolymer (F) was the minority component in the micelle core. On the other hand, when the F block exceeded the chain length of the hydrocarbon block (E), the superhydrophobic F block imposed a "double frustration" on the self-assembly of the mu-EOF(2-9-5) terpolymer; while F prefers to minimize its interfacial contact with the O corona, it must occupy the majority of the micellar core. Therefore, a richer variety of multicompartment micelles, including well-defined segmented worms, raspberry-like micelles, and multicompartmentalized worms, were formed from one terpolymer, as revealed by cryoTEM. Despite the complexity and variety of the observed aggregate morphologies, a small number of common structural elements can be invoked to interpret the observed micelles and to relate a given structure to the terpolymer composition.

Zhibo Li

Papers

Multicompartment micelles from ABC miktoarm stars in water.

Self-assembly of block copolymer micelles in an ionic liquid

Rapid formation of a supramolecular polypeptide-DNA Hydrogel for in situ three-dimensional multilayer bioprinting

Biodegradable stimuli-responsive polypeptide materials prepared by ring opening polymerization

Morphologies of multicompartment micelles formed by ABC miktoarm star terpolymers.