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

Many materials systems are currently under consideration as potential replacements for SiO2 as the gate dielectric material for sub-0.1 μm complementary metal–oxide–semiconductor (CMOS) technology. A systematic consideration of the required properties of gate dielectrics indicates that the key guidelines for selecting an alternative gate dielectric are (a) permittivity, band gap, and band alignment to silicon, (b) thermodynamic stability, (c) film morphology, (d) interface quality, (e) compatibility with the current or expected materials to be used in processing for CMOS devices, (f) process compatibility, and (g) reliability. Many dielectrics appear favorable in some of these areas, but very few materials are promising with respect to all of these guidelines. A review of current work and literature in the area of alternate gate dielectrics is given. Based on reported results and fundamental considerations, the pseudobinary materials systems offer large flexibility and show the most promise toward success...

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High-κ gate dielectrics: Current status and materials properties considerations

We present a new hybrid meta exchange-correlation functional, called M05-2X, for thermochemistry, thermochemical kinetics, and noncovalent interactions. We also provide a full discussion of the new M05 functional, previously presented in a short communication. The M05 functional was parametrized including both metals and nonmetals, whereas M05-2X is a high-nonlocality functional with double the amount of nonlocal exchange (2X) that is parametrized only for nonmetals. In particular, M05 was parametrized against 35 data values, and M05-2X is parametrized against 34 data values. Both functionals, along with 28 other functionals, have been comparatively assessed against 234 data values:  the MGAE109/3 main-group atomization energy database, the IP13/3 ionization potential database, the EA13/3 electron affinity database, the HTBH38/4 database of barrier height for hydrogen-transfer reactions, five noncovalent databases, two databases involving metal−metal and metal−ligand bond energies, a dipole moment databas...

/pdf/design-of-density-functionals-by-combining-the-method-of-3dsa6vb61i.pdf

Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions.

A single configuration model containing nonorthogonal magnetic orbitals is developed to represent the important features of the antiferromagnetic state of a transition metal dimer. A state of mixed spin symmetry and lowered space symmetry is constructed which has both conceptual and practical computational value. Either unrestricted Hartree–Fock theory or spin polarized density functional theory, e.g., Xα theory, can be used to generate the mixed spin state wave function. The most important consequence of the theory is that the Heisenberg exchange coupling constant J can be calculated simply from the energies of the mixed spin state and the highest pure spin multiplet.

Valence bond description of antiferromagnetic coupling in transition metal dimers

The direct (recomputation of two‐electron integrals) implementation of the gauge‐including atomic orbital (GIAO) and the CSGT (continuous set of gauge transformations) methods for calculating nuclear magnetic shielding tensors at both the Hartree‐Fock and density functional levels of theory are presented. Isotropic 13C, 15N, and 17O magnetic shielding constants for several molecules, including taxol (C47H51NO14 using 1032 basis functions) are reported. Shielding tensor components determined using the GIAO and CSGT methods are found to converge to the same value at sufficiently large basis sets; however, GIAO shielding tensor components for atoms other than carbon are found to converge faster with respect to basis set size than those determined using the CSGT method for both Hartree‐Fock and DFT. For molecules where electron correlation effects are significant, shielding constants determined using (gradient‐corrected) pure DFT or hybrid methods (including a mixture of Hartree‐Fock exchange and DFT exchange...

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A comparison of models for calculating nuclear magnetic resonance shielding tensors

Quantum Theory of Molecules and Solids Vol. 4: The Self‐Consistent Field for Molecules and Solids

An increasingly important issue in semiconductor device physics is understanding of how departures from ideal bonding at silicon–dielectric interfaces generate electrically active defects that limit performance and reliability Building on previously established criteria for formation of low defect density glasses, constraint theory is extended to crystalline silicon–dielectric interfaces that go beyond Si–SiO2 through development of a model that quantifies average bonding coordination at these interfaces This extension is validated by application to interfaces between Si and stacked silicon oxide/nitride dielectrics demonstrating that as in bulk glasses and thin films, an average coordination, Nav, greater than three yields increasing defective interfaces

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Bonding constraints and defect formation at interfaces between crystalline silicon and advanced single layer and composite gate dielectrics

Some four thousand years ago man discovered glass in the embers of a fire built somewhere in the deserts of the Near East. A few years from now ultratransparent glass fibers will be transmitting more information than copper wires. Thus glass is at once both one of the oldest and one of the newest materials known to civilization. Yet the science of glass is still in its infancy, and the most basic questions remain largely unanswered.

The Physics of glass

X-ray diffraction photographs of protein single crystals have been obtained using synchrotron radiation produced by an electron-positron storage ring. The diffracted intensities observed with this unconventional source are a factor of at least 60 greater than those obtained with a sealed x-ray tube using the same crystal and instrumental parameters. Diffraction data have been collected by the precession method to higher resolution and using smaller protein crystals than would have been possible with a conventional source. The crystal decay rate in the synchrotron beam for several proteins appears to be substantially less than that observed with Ni-filtered Cu radiation. The tunable nature of the source (which allows selective optimization of anomalous contributions to the scattering factors) and the low angular divergence of the beam make the source very useful for single crystal protein diffraction studies.

https://www.pnas.org/content/pnas/73/1/128.full.pdf

Applications of synchrotron radiation to protein crystallography: preliminary results

Self-organized criticality, a powerful concept, originated in 1987 as an extension of fractal geometries to thermodynamic systems in the vicinities of instabilities. The value of fractal methods can be greatly enhanced in realistic models that exploit accurate fractal values derived from homogeneous (possibly curated) Big Data. We illustrate this point by discussing the derivation of fractal exponents describing protein–water interactions, and their application to protein roughness, protein binding and potentially protein engineering. The examples studied are evolution of lysozyme c and acylphosphatase, and mutational effects on their aggregation.

James C. Phillips

Papers

Quantum Theory of Molecules and Solids Vol. 4: The Self‐Consistent Field for Molecules and Solids

Bonding constraints and defect formation at interfaces between crystalline silicon and advanced single layer and composite gate dielectrics

The Physics of glass

Applications of synchrotron radiation to protein crystallography: preliminary results

Fractals and self-organized criticality in proteins