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

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

A living radical polymerization (LRP) is a free radical polymerization that aims at displaying living character, (i.e., does not terminate or transfer and is able to continue polymerization once the initial feed is exhausted by addition of more monomer). However, termination reactions are inherent to a radical process, and modern LRP techniques seek to minimize such reactions, therefore providing control over the molecular weight and the molecular weight distribution of a polymeric material. In addition, the better LRP techniques incorporate many of the desirable features of traditional free radical polymerization, such as compatibility with a wide range of monomers, tolerance of many functionalities, and facile reaction conditions. The control of molecular weight and molecular weight distribution has enabled access to complex architectures and site specific functionality that were previously impossible to achieve via traditional free radical polymerizations. These LRPs are classified in three different subgroups: (1) stable free-radical polymerization such as nitroxide mediated polymerization (NMP),1,2 (2) degenerative transfer polymerization, such as iodine transfer polymerization (ITP and RITP),3,4 single electron transfer-degenerative transfer living radical polymerization(SET-DTLRP),5,6reversibleaddition-fragmentation chain transfer (RAFT),7,8 and macromolecular design via the interchange of xanthates (MADIX)9,10 polymerization, and (3) metal mediated catalyzed polymerization, such as atom transfer radical polymerization (ATRP),11-14 single electron transfer-living radical polymerization (SET-LRP),15 and organotellurium mediated living radical polymrization16-19 Among the existing LRP techniques, RAFT and MADIX are probably the most versatile processes, as they are tolerant * E-mail: T.P.D., T.Davis@UNSW.edu.au; S.P., S.Perrier@ chem.usyd.edu.au. † Centre for Advanced Macromolecular Design (CAMD), School of Chemical Sciences & Engineering, UNSW. ‡ Centre for Advanced Macromolecular Design (CAMD), School of Biotechnology & Biomolecular Sciences, UNSW. § The University of Sydney. Chem. Rev. 2009, 109, 5402–5436 5402

Bioapplications of RAFT polymerization.

Challenges and breakthroughs in recent research on self-assembly

The last two decades have witnessed an upsurge of research activities in the area of supramolecular gelators, especially low molecular mass organic gelators (LMOGs), not only for academic interests but also for their potential applications in materials science. However, most of the gelators are serendipitously obtained; their rational design and synthesis is still a major challenge. Wide structural diversities of the molecules known to act as LMOGs and a dearth of molecular level understanding of gelation mechanisms make it difficult to pin-point a particular strategy to achieve rational design of gelators. Nevertheless, some efforts are being made to achieve this goal. Once a gelling agent is serendipitously obtained, new gelling agents with novel properties may be prepared by modifying the parent gelator molecule following a molecular engineering rationale; however, such approach is limited to the same class of gelling agent generated from the parent gelating scaffold. A crystal engineering approach wherein the single-crystal structure of a molecule is correlated with its gelling/nongelling behaviour (structure–property correlation) allows molecular level understandings of the self-assembly of the gelator and nongelator molecules and therefore, provides new insights into the design aspects of supramolecular gelling agents. This tutorial review aims at highlighting some of the developments covering both molecular and crystal engineering approaches in designing LMOGs.

Supramolecular gelling agents: can they be designed?

A strong beta-sheet forming peptide was conjugated to PEO and utilized to guide the structure formation process toward well-defined, tape-like structures with millimeters in length, about 2 mum width, and approximately 50 nm height. The aggregation tendency of the peptide was temporarily suppressed for ease of synthesis by the integration of multiple switch-peptide defect segments into the peptide backbone. A subsequent rearrangement in the defects re-establishes the native peptide backbone and triggers the assembly by switching the aggregation properties on.

Switch-peptides to trigger the peptide guided assembly of poly(ethylene oxide)-peptide conjugates into tape structures

Synthesis and peptide-guided self-assembly of an organo-soluble peptide−polymer conjugate, comprising a sequence-defined polypeptide and a poly(n-butyl acrylate), are described. The amino acid sequence of the peptide encodes a high tendency to adopt an antiparallel β-sheet motif, and thus programs the formation of tapelike microstructures. Easy synthesis and controllable self-assembly is ensured by the incorporation of structure breaking switch defects into the peptide segment. This suppresses temporarily the aggregation tendency of the conjugate as shown by circular dichroism, infrared spectroscopy (FT-IR), and atomic force microscopy (AFM). A pH-controlled rearrangement in the switch segments restores the native peptide backbone, triggering the self-assembly process and leading to the formation of densely twisted tapelike microstructures as could be observed by AFM and transmission electron microscopy. The resulting helical superstructures, when deposited on a substrate, are 2.9 nm high, 10 nm wide, and...

Peptide-Directed Microstructure Formation of Polymers in Organic Media

Oligothiophene versus beta-sheet peptide : synthesis and self-assembly of an organic semiconductor-peptide hybrid

Easy access to bioactive peptide-polymer conjugates via RAFT

The synthesis and self-assembly behavior of a set of peptide−polymer conjugates is described. It is demonstrated that an oligopeptide segment, composing 3.5 wt % of a conjugate, can effectively dir...

Jens Hentschel

Papers

Switch-peptides to trigger the peptide guided assembly of poly(ethylene oxide)-peptide conjugates into tape structures

Peptide-Directed Microstructure Formation of Polymers in Organic Media

Oligothiophene versus beta-sheet peptide : synthesis and self-assembly of an organic semiconductor-peptide hybrid

Easy access to bioactive peptide-polymer conjugates via RAFT

Peptide-guided organization of peptide-polymer conjugates: Expanding the approach from oligo- to polymers