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 unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

The bulk-heterojunction blend of an electron donor and an electron acceptor material is the key component in a solution-processed organic photovoltaic device. In the past decades, a p-type conjugated polymer and an n-type fullerene derivative have been the most commonly used electron donor and electron acceptor, respectively. While most advances of the device performance come from the design of new polymer donors, fullerene derivatives have almost been exclusively used as electron acceptors in organic photovoltaics. Recently, nonfullerene acceptor materials, particularly small molecules and oligomers, have emerged as a promising alternative to replace fullerene derivatives. Compared to fullerenes, these new acceptors are generally synthesized from diversified, low-cost routes based on building block materials with extraordinary chemical, thermal, and photostability. The facile functionalization of these molecules affords excellent tunability to their optoelectronic and electrochemical properties. Within t...

Nonfullerene Acceptor Molecules for Bulk Heterojunction Organic Solar Cells

Organic (opto)electronic materials have received considerable attention due to their applications in thin-film-transistors, light-emitting diodes, solar cells, sensors, photorefractive devices, and many others. The technological promises include low cost of these materials and the possibility of their room-temperature deposition from solution on large-area and/or flexible substrates. The article reviews the current understanding of the physical mechanisms that determine the (opto)electronic properties of high-performance organic materials. The focus of the review is on photoinduced processes and on electronic properties important for optoelectronic applications relying on charge carrier photogeneration. Additionally, it highlights the capabilities of various experimental techniques for characterization of these materials, summarizes top-of-the-line device performance, and outlines recent trends in the further development of the field. The properties of materials based both on small molecules and on conjug...

Organic Optoelectronic Materials: Mechanisms and Applications

Direct visualization of the motion of long-lived charge-transfer states in an organic blend reveals that bound electron–hole pairs stretch and contract, and diffuse more than 10 nm before they dissociate or recombine.

Nanoscale transport of charge-transfer states in organic donor-acceptor blends

Noticeable differences between the vibrational (IR and Raman) spectra of neat H2O and D2O ice Ih are observed experimentally. Here, we employ our theoretical mixed quantum/classical approach to investigate these differences. We find reasonable agreement between calculated and experimental line shapes at both high and low temperatures. From understanding the structure of ice Ih and its vibrational exciton Hamiltonian, we provide assignments of the IR and Raman spectral features for both H2O and D2O ice Ih. We find that in H2O ice these features are due to strong and weak intermolecular coupling, not to intramolecular coupling. The differences between H2O and D2O ice spectra are attributed to the significantly stronger intramolecular coupling in D2O ice. Our conclusion for both H2O and D2O ice is that the molecular symmetric and antisymmetric normal modes do not form a useful basis for understanding OH or OD stretch spectroscopy.

Interpretation of IR and Raman Line Shapes for H2O and D2O Ice Ih

We present a unified picture of how OH-stretch spectroscopy in water can be understood in terms of hydrogen bonding for the four systems listed in the title. To understand the strength, and hence OH-stretch frequency, of a hydrogen bond, it is crucial to consider the number of additional acceptor hydrogen bonds made by both the donor and acceptor molecules. This necessity for focusing on the hydrogen-bond environment of both donor and acceptor molecules follows from quantum chemical considerations and is related to the three-body interactions in water. Armed with this understanding we can make a detailed interpretation of the OH-stretch IR absorption spectrum of the cage conformer for HOD(D2O)5 and the imaginary part of the ssp OH-stretch sum-frequency spectrum of the surface of liquid D2O with dilute HOD.

Hydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and Ice

Infrared spectroscopy of the water OH stretch provides a sensitive probe of the local hydrogen-bonding structure and dynamics of water molecules. Previously, we have utilized a mixed quantum/classical model to calculate vibrational spectroscopic observables for bulk water, ice, the liquid/vapor interface, and small water clusters, as well as water interacting with ions and biological molecules. These studies rely on spectroscopic maps that relate the OH stretching frequency and transition dipole to the local environment around a water molecule. Our spectroscopic maps were parametrized based on water clusters taken from bulk water simulations; in this article, we test the robustness of these maps for water in nonbulk-liquid environments. We find that the frequency, transition dipole, and coupling maps work as well for the water surface, ice Ih, and the water hexamer as they do for liquid water. This suggests that these maps may be generally applied to study the vibrational spectroscopy of water in diverse,...

Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy.

In this study, we present the third version of a water model that explicitly includes three-body interactions. The major difference between this version and the previous two is in the two-body water model we use as a reference potential; here we use the TIP4P/2005 model (previous versions used the TIP4P water model). We alter four parameters from our previous version of the model by fitting to the diffusion coefficient of the ambient liquid, the liquid and ice densities, and the melting point. We evaluate the performance of this version by calculating many other microscopic and thermodynamic static and dynamic properties as a function of temperature and near the critical point and comparing to experiment, the TIP4P/2005 model and the previous version of our three-body model.

Liang Shi

Papers

Nanoscale transport of charge-transfer states in organic donor-acceptor blends

Interpretation of IR and Raman Line Shapes for H2O and D2O Ice Ih

Hydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and Ice

Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy.

Reparametrized E3B (Explicit Three-Body) Water Model Using the TIP4P/2005 Model as a Reference.