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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Dye-sensitized solar cells (DSCs) offer the possibilities to design solar cells with a large flexibility in shape, color, and transparency. DSC research groups have been established around the worl ...

/pdf/dye-sensitized-solar-cells-50b0w2bhsr.pdf

Dye-Sensitized Solar Cells

http://theory.cm.utexas.edu/henkelman/pubs/henkelman06_354.pdf

A fast and robust algorithm for Bader decomposition of charge density

A computational method for partitioning a charge density grid into Bader volumes is presented which is efficient, robust, and scales linearly with the number of grid points. The partitioning algorithm follows the steepest ascent paths along the charge density gradient from grid point to grid point until a charge density maximum is reached. In this paper, we describe how accurate off-lattice ascent paths can be represented with respect to the grid points. This improvement maintains the efficient linear scaling of an earlier version of the algorithm, and eliminates a tendency for the Bader surfaces to be aligned along the grid directions. As the algorithm assigns grid points to charge density maxima, subsequent paths are terminated when they reach previously assigned grid points. It is this grid-based approach which gives the algorithm its efficiency, and allows for the analysis of the large grids generated from plane-wave-based density functional theory calculations.

/pdf/a-grid-based-bader-analysis-algorithm-without-lattice-bias-4zdxoor5iz.pdf

A grid-based Bader analysis algorithm without lattice bias

The result of a calculation of excited states, be it via configuration interaction methods or density functional response theory, is a set of coefficients describing the contribution that individual orbital excitations make to the total transition. Often times, there is no dominant amplitude describing the transition, making its qualitative description difficult. Natural transition orbitals dramatically simplify the situation by providing a compact representation of the transition density matrix. This is accomplished using the corresponding orbital transformation of Amos and Hall, which renders the transition density matrix diagonal and provides a unique correspondence between the excited ‘particle’ and empty ‘hole’.


Keywords:

natural transition orbital;
transition density matrix;
corresponding orbital transformation;
singular value decomposition

Natural Transition Orbitals

Density Functional calculations have been performed to calculate the one-electron oxidation potential for ferrocene and the redox couples for a series of small transition metal compounds of the first-, second-, and third-row elements. The solvation effects are incorporated via a self-consistent reaction field (SCRF), using the polarized continuum model (PCM). From our study of seven different density functionals combined with three different basis sets for ferrocene, we find that no density functional method can reproduce the redox trends from experiment when referencing our results to the experimental absolute standard hydrogen electrode (SHE) potential. In addition, including additional necessary assumptions such as solvation effects does not lead to any conclusion regarding the appropriate functional. However, we propose that if one references their transition metal compounds results to the calculated absolute half-cell potential of ferrocene, they can circumvent the additional assumptions necessary to...

Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?

Here we describe the synthesis of two imido analogs of the uranyl ion, UO2+2, in which the oxygens are replaced by divalent alkyl or aryl nitrogen groups: U(NtBu)2I2(THF)2 (1) and U(NPh)2I2(THF)3 (2) (where tBu is tert-butyl and THF is tetrahydrofuran). Both compounds have been fully characterized by standard analytical techniques, including x-ray crystallography, and the chemical bonding between the metal center and the nitrogen ligands was quantified by using hybrid density functional theory calculations. As expected for a uranyl analog, these complexes exhibit linear N-U-N linkages and very short U-N bonds. In addition, the theoretical calculations show strong involvement of the 5f and 6d electrons in the U-N bonding.

https://science.sciencemag.org/content/sci/310/5756/1941.full.pdf

Synthesis of imido analogs of the uranyl ion.

Uranium nitride [U[triple bond]N](x) is an alternative nuclear fuel that has great potential in the expanding future of nuclear power; however, very little is known about the U[triple bond]N functionality. We show, for the first time, that a terminal uranium nitride complex can be generated by photolysis of an azide (U-N=N=N) precursor. The transient U[triple bond]N fragment is reactive and undergoes insertion into a ligand C-H bond to generate new N-H and N-C bonds. The mechanism of this unprecedented reaction has been evaluated through computational and spectroscopic studies, which reveal that the photochemical azide activation pathway can be shut down through coordination of the terminal azide ligand to the Lewis acid B(C(6)F(5))(3). These studies demonstrate that photochemistry can be a powerful tool for inducing redox transformations for organometallic actinide complexes, and that the terminal uranium nitride fragment is reactive, cleaving strong C-H bonds.

/pdf/uranium-azide-photolysis-results-in-c-h-bond-activation-and-3lwohgcca2.pdf

Uranium azide photolysis results in C–H bond activation and provides evidence for a terminal uranium nitride

We have used an induction model including dipole, dipole–quadrupole, quadrupole–quadrupole polarizability and first hyperpolarizability as well as fixed octopole and hexadecapole moments to study the electric field in ice. The self-consistent induction calculations gave an average total dipole moment of 3.09 D, a 67% increase over the dipole moment of an isolated water molecule. A previous, more approximate induction model study by Coulson and Eisenberg [Proc. R. Soc. Lond. A 291, 445 (1966)] suggested a significantly smaller average value of 2.6 D. This value has been used extensively in recent years as a reference point in the development of various polarizable interaction potentials for water as well as for assessment of the convergence of water cluster properties to those of bulk. The reason for this difference is not due to approximations made in the computational scheme of Coulson and Eisenberg but rather due to the use of less accurate values for the molecular multipoles in these earlier calculations.

/pdf/molecular-multipole-moments-of-water-molecules-in-ice-ih-7q41e2lzrf.pdf

Enrique R. Batista

Papers

Natural Transition Orbitals

Calculation of One-Electron Redox Potentials Revisited. Is It Possible to Calculate Accurate Potentials with Density Functional Methods?

Synthesis of imido analogs of the uranyl ion.

Uranium azide photolysis results in C–H bond activation and provides evidence for a terminal uranium nitride

Molecular multipole moments of water molecules in ice Ih