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 previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

We present the results of mixed quantum/classical simulations on relaxed thermal nanoscale water cluster anions, (H(2)O)(n)(-), with n=200, 500, 1000, and 8000. By using initial equilibration with constraints, we investigate stable/metastable negatively charged water clusters with both surface-bound and interior-bound excess electron states. Characterization of these states is performed in terms of geometrical parameters, energetics, and optical absorption spectroscopy of the clusters. The calculations provide data characterizing these states in the gap between previously published calculations and experiments on smaller clusters and the limiting cases of either an excess electron in bulk water or an excess electron at an infinite water/air interface. The present results are in general agreement with previous simulations and provide a consistent picture of the evolution of the physical properties of water cluster anions with size over the entire size range, including results for vertical detachment energies and absorption spectra that would signify their presence. In particular, the difference in size dependence between surface-bound and interior-bound state absorption spectra is dramatic, while for detachment energies the dependence is qualitatively the same.

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Interior- and surface-bound excess electron states in large water cluster anions.

The accuracy of the HNC approximation and modifications based on a simple approximation for the sum of bridge graphs has been studied for a charged soft sphere model for dilute aqueous 2‐2 electrolytes. The accuracy is judged based on extensive Monte Carlo (MC) simulation for three representative concentrations: 0.005, 0.0625, and 0.2 M. The MC simulations find monotonically increasing like‐charge correlation functions in agreement with the modified HNC results but in contrast with the HNC prediction of a local maximum at low concentration. Nevertheless, HNC provides the best overall quantitative match with MC except at very low concentration; at 5 mM the modifications are a significant improvement. For unlike charge correlations, there is good agreement among all methods; at the ionic contact peak, however, HNC underestimates the peak height and the modifications provide improved accuracy.

Corrections to the HNC equation for associating electrolytes

Computer simulation study of an sn2 reaction in supercritical water

Conjugated polymers in the solid state usually exhibit low fluorescence quantum yields, which limit their applications in many areas such as light-emitting diodes. Despite considerable research efforts, the underlying mechanism still remains controversial and elusive. Here, the nature and properties of excited states in the archetypal polythiophene are investigated via aggregates suspended in solvents with different dielectric constants (ɛ). In relatively polar solvents (ɛ>∼ 3), the aggregates exhibit a low fluorescence quantum yield (QY) of 2-5%, similar to bulk films, however, in relatively nonpolar solvents (ɛ<∼ 3) they demonstrate much higher fluorescence QY up to 20-30%. A series of mixed quantum-classical atomistic simulations illustrate that dielectric induced stabilization of nonradiative charge-transfer (CT) type states can lead to similar drastic reduction in fluorescence QY as seen experimentally. Fluorescence lifetime measurement reveals that the CT-type states exist as a competitive channel of the formation of emissive exciton-type states.

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An insight into non-emissive excited states in conjugated polymers

Recent reports have demonstrated that the correlation function of the fluorescence dichroism signal, measured as a probe of single molecule rotational dynamics, should not manifest a single exponential decay even for isotropic diffusion. This has called into question the attribution of observed nonexponential behavior in supercooled fluids and polymer systems to dynamical heterogeneity. We show here that, for the case of a high numerical aperture objective, the dichroism decay becomes indistinguishable from a single exponential. As a consequence, observed nonexponential decays can be associated with complex rotational dynamics. These effects are illustrated via simulated rotational trajectories for isotropic diffusion of a dipole.

Peter J. Rossky

Papers

Interior- and surface-bound excess electron states in large water cluster anions.

Corrections to the HNC equation for associating electrolytes

Computer simulation study of an sn2 reaction in supercritical water

An insight into non-emissive excited states in conjugated polymers

Origins of nonexponential decay in single molecule measurements of rotational dynamics.