There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

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

The exact density functional for the ground-state energy is strictly self-interaction-free (i.e., orbitals demonstrably do not self-interact), but many approximations to it, including the local-spin-density (LSD) approximation for exchange and correlation, are not. We present two related methods for the self-interaction correction (SIC) of any density functional for the energy; correction of the self-consistent one-electron potenial follows naturally from the variational principle. Both methods are sanctioned by the Hohenberg-Kohn theorem. Although the first method introduces an orbital-dependent single-particle potential, the second involves a local potential as in the Kohn-Sham scheme. We apply the first method to LSD and show that it properly conserves the number content of the exchange-correlation hole, while substantially improving the description of its shape. We apply this method to a number of physical problems, where the uncorrected LSD approach produces systematic errors. We find systematic improvements, qualitative as well as quantitative, from this simple correction. Benefits of SIC in atomic calculations include (i) improved values for the total energy and for the separate exchange and correlation pieces of it, (ii) accurate binding energies of negative ions, which are wrongly unstable in LSD, (iii) more accurate electron densities, (iv) orbital eigenvalues that closely approximate physical removal energies, including relaxation, and (v) correct longrange behavior of the potential and density. It appears that SIC can also remedy the LSD underestimate of the band gaps in insulators (as shown by numerical calculations for the rare-gas solids and CuCl), and the LSD overestimate of the cohesive energies of transition metals. The LSD spin splitting in atomic Ni and $s\ensuremath{-}d$ interconfigurational energies of transition elements are almost unchanged by SIC. We also discuss the admissibility of fractional occupation numbers, and present a parametrization of the electron-gas correlation energy at any density, based on the recent results of Ceperley and Alder.

Self-interaction correction to density-functional approximations for many-electron systems

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a highly flexible computer program which uses empirical energy functions to model macromolecular systems. The program can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations. The operations that CHARMM can perform are described, and some implementation details are given. A set of parameters for the empirical energy function and a sample run are included.

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

An exact stochastic simulation of the Schroedinger equation for charged Bosons and Fermions was used to calculate the correlation energies, to locate the transitions to their respective crystal phases at zero temperature within 10%, and to establish the stability at intermediate densities of a ferromagnetic fluid of electrons.

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Ground state of the electron gas by a stochastic method

One of Feynman's early applications of path integrals was to superfluid $^{4}\mathrm{He}$. He showed that the thermodynamic properties of Bose systems are exactly equivalent to those of a peculiar type of interacting classical "ring polymer." Using this mapping, one can generalize Monte Carlo simulation techniques commonly used for classical systems to simulate boson systems. In this review, the author introduces this picture of a boson superfluid and shows how superfluidity and Bose condensation manifest themselves. He shows the excellent agreement between simulations and experimental measurements on liquid and solid helium for such quantities as pair correlations, the superfluid density, the energy, and the momentum distribution. Major aspects of computational techniques developed for a boson superfluid are discussed: the construction of more accurate approximate density matrices to reduce the number of points on the path integral, sampling techniques to move through the space of exchanges and paths quickly, and the construction of estimators for various properties such as the energy, the momentum distribution, the superfluid density, and the exchange frequency in a quantum crystal. Finally the path-integral Monte Carlo method is compared to other quantum Monte Carlo methods.

Path integrals in the theory of condensed helium

The ground‐state energies of H2, LiH, Li2, and H2O are calculated by a fixed‐node quantum Monte Carlo method, which is presented in detail. For each molecule, relatively simple trial wave functions ΨT are chosen. Each ΨT consists of a single Slater determinant of molecular orbitals multiplied by a product of pair‐correlation (Jastrow) functions. These wave functions are used as importance functions in a stochastic approach that solves the Schrodinger equation by treating it as a diffusion equation. In this approach, ΨT serves as a ‘‘guiding function’’ for a random walk of the electrons through configuration space. In the fixed‐node approximation used here, the diffusion process is confined to connected regions of space, bounded by the nodes (zeros) of ΨT. This approximation simplifies the treatment of Fermi statistics, since within each region an electronic probability amplitude is obtained which does not change sign. Within these approximate boundaries, however, the Fermi problem is solved exactly. The e...

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Fixed-node quantum Monte Carlo for molecules

Variational and fixed-node Green's-function Monte Carlo calculations have been performed to find the ground-state properties of the two-dimensional electron gas in the density range 1\ensuremath{\le}${r}_{s}$\ensuremath{\le}100. Our calculations predict a Wigner crystallization at the density ${r}_{s}$\ensuremath{\simeq}37\ifmmode\pm\else\textpm\fi{}5. The electron system is found to be in the normal- (paramagnetic) fluid state below the transition density, but the fully polarized state is very close in energy. We have tabulated the values of pair distribution function g(r), the static structure factor S(k), and the momentum distribution n(k) at several densities of interest both in the normal and the polarized phases. An estimate of the spin susceptibility \ensuremath{\chi} is also given.

Ground state of the two-dimensional electron gas

The Metropolis Monte Carlo method is used to sample the square of an antisymmetric wave function composed of a product of a Jastrow wave function and a number of Slater determinants. We calculate variational energies for $^{3}\mathrm{He}$ and several models of neutron matter. The first-order Wu-Feenberg expansion is shown always to underestimate the energy, sometimes seriously. The phase diagram for ground-state Yukawa matter is determined. There is a class of Yukawa potentials which do not lead to a crystal phase at any density.

David M. Ceperley

Papers

Ground state of the electron gas by a stochastic method

Path integrals in the theory of condensed helium

Fixed-node quantum Monte Carlo for molecules

Ground state of the two-dimensional electron gas

Monte Carlo simulation of a many-fermion study