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

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

Quantification of biological or biochemical processes are of utmost importance for medical, biological and biotechnological applications. However, converting the biological information to an easily processed electronic signal is challenging due to the complexity of connecting an electronic device directly to a biological environment. Electrochemical biosensors provide an attractive means to analyze the content of a biological sample due to the direct conversion of a biological event to an electronic signal. Over the past decades several sensing concepts and related devices have been developed. In this review, the most common traditional techniques, such as cyclic voltammetry, chronoamperometry, chronopotentiometry, impedance spectroscopy, and various field-effect transistor based methods are presented along with selected promising novel approaches, such as nanowire or magnetic nanoparticle-based biosensing. Additional measurement techniques, which have been shown useful in combination with electrochemical detection, are also summarized, such as the electrochemical versions of surface plasmon resonance, optical waveguide lightmode spectroscopy, ellipsometry, quartz crystal microbalance, and scanning probe microscopy. The signal transduction and the general performance of electrochemical sensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor. New nanotechnology-based approaches, such as the use of engineered ion-channels in lipid bilayers, the encapsulation of enzymes into vesicles, polymersomes, or polyelectrolyte capsules provide additional possibilities for signal amplification. In particular, this review highlights the importance of the precise control over the delicate interplay between surface nano-architectures, surface functionalization and the chosen sensor transducer principle, as well as the usefulness of complementary characterization tools to interpret and to optimize the sensor response.

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Electrochemical Biosensors - Sensor Principles and Architectures

2.2.1. Polyisocyanates 6117 2.2.2. Polysilanes 6118 2.2.3. Polyacetylenes 6120 2.3. Foldamer-Based Helical Polymers 6124 2.3.1. Click Polymerization 6126 2.3.2. Ring-Closing Reaction 6126 2.4. Other Types of Helical Polymers 6127 2.4.1. π-Conjugated Helical Polymers 6127 2.4.2. Metallosupramolecular Helical Polymers 6128 2.5. Induced Helical Polymers 6130 2.5.1. Induced Helical Polyacetylenes 6130 2.5.2. Other Induced Helical Polymers and Oligomers 6132

Helical polymers: synthesis, structures, and functions

In this comprehensive review, recent progress and developments on perfluorinated sulfonic-acid (PFSA) membranes have been summarized on many key topics. Although quite well investigated for decades, PFSA ionomers’ complex behavior, along with their key role in many emerging technologies, have presented significant scientific challenges but also helped create a unique cross-disciplinary research field to overcome such challenges. Research and progress on PFSAs, especially when considered with their applications, are at the forefront of bridging electrochemistry and polymer (physics), which have also opened up development of state-of-the-art in situ characterization techniques as well as multiphysics computation models. Topics reviewed stem from correlating the various physical (e.g., mechanical) and transport properties with morphology and structure across time and length scales. In addition, topics of recent interest such as structure/transport correlations and modeling, composite PFSA membranes, degradat...

Akihiro Ohira

Papers

Hydration behavior of perfluorinated and hydrocarbon-type proton exchange membranes: Relationship between morphology and proton conduction

Free volume and permeabilities of O2 and H2 in Nafion membranes for polymer electrolyte fuel cells

A two-dimensional molecular network structure of trimesic acid prepared by adsorption-induced self-organization

Versatile Helical Polymer Films: Chiroptical Inversion Switching and Memory with Re‐Writable (RW) and Write‐Once Read‐Many (WORM) Modes

Electrochemical, AFM and QCM studies on ferritin immobilized onto a self-assembled monolayer-modified gold electrode