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

Glasses can be formed by many routes. In some cases, distinct polyamorphic forms are found. The normal mode of glass formation is cooling of a viscous liquid. Liquid behavior during cooling is classified between "strong" and "fragile," and the three canonical characteristics of relaxing liquids are correlated through the fragility. Strong liquids become fragile liquids on compression. In some cases, such conversions occur during cooling by a weak first-order transition. This behavior can be related to the polymorphism in a glass state through a recent simple modification of the van der Waals model for tetrahedrally bonded liquids. The sudden loss of some liquid degrees of freedom through such first-order transitions is suggestive of the polyamorphic transition between native and denatured hydrated proteins, which can be interpreted as single-chain glass-forming polymers plasticized by water and cross-linked by hydrogen bonds. The onset of a sharp change in d dT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature. The latter may originate in strong anharmonicity in modes ("bosons"), which permits the system to access multiple minima of its configuration space. These modes, the Kauzmann temperature T(K), and the fragility of the liquid, may thus be connected.

https://science.sciencemag.org/content/sci/267/5206/1924.full.pdf

Formation of glasses from liquids and biopolymers.

Small but strong: A review of the mechanical properties of carbon nanotube–polymer composites

I read this book the same weekend that the Packers took on the Rams, and the experience of the latter event, obviously, colored my judgment. Although I abhor anything that smacks of being a handbook (like, \"How to Earn a Merit Badge in Neurosurgery\") because too many volumes in biomedical science already evince a boyscout-like approach, I must confess that parts of this volume are fast, scholarly, and significant, with certain reservations. I like parts of this well-illustrated book because Dr. Sj6strand, without so stating, develops certain subjects on technique in relation to the acquisition of judgment and sophistication. And this is important! So, given that the author (like all of us) is somewhat deficient in some areas, and biased in others, the book is still valuable if the uninitiated reader swallows it in a general fashion, realizing full well that what will be required from the reader is a modulation to fit his vision, propreception, adaptation and response, and the kind of problem he is undertaking. A major deficiency of this book is revealed by comparison of its use of physics and of chemistry to provide understanding and background for the application of high resolution electron microscopy to problems in biology. Since the volume is keyed to high resolution electron microscopy, which is a sophisticated form of structural analysis, but really morphology in a modern guise, the physical and mechanical background of The instrument and its ancillary tools are simply and well presented. The potential use of chemical or cytochemical information as it relates to biological fine structure , however, is quite deficient. I wonder when even sophisticated morphol-ogists will consider fixation a reaction and not a technique; only then will the fundamentals become self-evident and predictable and this sine qua flon will become less mystical. Staining reactions (the most inadequate chapter) ought to be something more than a technique to selectively enhance contrast of morphological elements; it ought to give the structural addresses of some of the chemical residents of cell components. Is it pertinent that auto-radiography gets singled out for more complete coverage than other significant aspects of cytochemistry by a high resolution microscopist, when it has a built-in minimal error of 1,000 A in standard practice? I don't mean to blind-side (in strict football terminology) Dr. Sj6strand's efforts for what is \"routinely used in our laboratory\"; what is done is usually well done. It's just that …

Methods in Enzymology.

Carbon nanotube–polymer composites: Chemistry, processing, mechanical and electrical properties

Low-frequency Raman spectra of strong and fragile glass forming liquids were measured in a wide temperature range. From an analysis of the spectra and literature data it is found that the main difference in the dynamic structure factor is the ratio of vibrational to relaxational contributions: The stronger the glass former the higher this ratio. It is shown that this difference survives even at very low temperatures and determines the low-temperature anomalies of glasses. A possible way how the observed difference influences the fragility of a liquid is discussed.

Dynamics of strong and fragile glass formers: Differences and correlation with low-temperature properties.

The correlation lengths of vitreous structures estimated from the low-frequency (boson) peak in Raman spectra and from the width of the first sharp diffraction peak are compared. This first comparison shows that the two estimates, which are based on dynamic and static properties, respectively, are in good quantitative agreement. The present result supports the concepts that (a) a decisive scale for structural order in glasses is \ensuremath{\sim}10 \AA{}, and (b) the low-frequency excitations are defined by the characteristic length in vitreous structures.

Medium-range order in glasses: Comparison of Raman and diffraction measurements.

Microscopic Mechanism of reinforcement in single-wall carbon nanotube/polypropylene nanocomposite

Conductivity and mechanical properties of well-dispersed single-wall carbon nanotube/polystyrene composite

It is generally believed that the strength of the polymer–nanoparticle interaction controls the modification of near-interface segmental mobility in polymer nanocomposites (PNCs). However, little is known about the effect of covalent bonding on the segmental dynamics and glass transition of matrix-free polymer-grafted nanoparticles (PGNs), especially when compared to PNCs. In this article, we directly compare the static and dynamic properties of poly(2-vinylpyridine)/silica-based nanocomposites with polymer chains either physically adsorbed (PNCs) or covalently bonded (PGNs) to identical silica nanoparticles (RNP = 12.5 nm) for three different molecular weight (MW) systems. Interestingly, when the MW of the matrix is as low as 6 kg/mol (RNP/Rg = 5.4) or as high as 140 kg/mol (RNP/Rg= 1.13), both small-angle X-ray scattering and broadband dielectric spectroscopy show similar static and dynamic properties for PNCs and PGNs. However, for the intermediate MW of 18 kg/mol (RNP/Rg = 3.16), the difference betwee...

Alexander Kisliuk

Papers

Dynamics of strong and fragile glass formers: Differences and correlation with low-temperature properties.

Medium-range order in glasses: Comparison of Raman and diffraction measurements.

Microscopic Mechanism of reinforcement in single-wall carbon nanotube/polypropylene nanocomposite

Conductivity and mechanical properties of well-dispersed single-wall carbon nanotube/polystyrene composite

Controlling Interfacial Dynamics: Covalent Bonding versus Physical Adsorption in Polymer Nanocomposites