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

Because of its fundamental importance in many branches of science, hydrogen bonding is a subject of intense contemporary research interest. The physical and chemical properties of hydrogen bonds in the ground state have been widely studied both experimentally and theoretically by chemists, physicists, and biologists. However, hydrogen bonding in the electronic excited state, which plays an important role in many photophysical processes and photochemical reactions, has scarcely been investigated.Upon electronic excitation of hydrogen-bonded systems by light, the hydrogen donor and acceptor molecules must reorganize in the electronic excited state because of the significant charge distribution difference between the different electronic states. The electronic excited-state hydrogen-bonding dynamics, which are predominantly determined by the vibrational motions of the hydrogen donor and acceptor groups, generally occur on ultrafast time scales of hundreds of femtoseconds. As a result, state-of-the-art femtos...

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Hydrogen Bonding in the Electronic Excited State

Recent research has indicated that fluorescent probes have tremendous potential for the selective detection of chemical and biological species. Over the past decade, researchers have proposed a series of fluorescence‐based sensing mechanisms of such probes by the calculation of their electronic excited states. Investigations of sensing mechanisms have been based on deep insights into the interactions between probe molecules and their target species, as well as their fluorescence properties. Advances in calculation methods, modeling software, and computational power have enabled researchers to use excited‐state theoretical calculations to reproduce experimental fluorescence phenomena and then provide molecular‐level explanations thereof. In this advanced review, we describe the evolution of theoretical studies on excited‐state sensing mechanisms for fluorescent probes that respond to target species. Focusing on calculation methods that facilitate investigation of the photophysical properties and excited‐state dynamics of probes, we emphasize sensing mechanisms mainly reported by our group. Most of these studies have been supported by theoretical predictions based on time‐dependent density functional theory. For this most popular excited‐state calculation method, vertical excitation energy, excited‐state geometrical optimization and a scan of the excited‐state potential energy surface should be noted in the calculation of electronic and molecular differences between the excited‐state probe and its reaction product with the target analyte. These state‐of‐the‐art calculations are of great importance for unraveling details of fluorescence‐based sensing mechanisms, including photochemical reactions (such as twist intramolecular charge transfer and excited‐state proton transfer) and excited‐state electronic processes (such as intramolecular charge transfer and photoinduced electron transfer). These studies have generated new and inspirational mechanistic proposals and have provided a systematic approach for the development of efficient fluorescent sensors. WIREs Comput Mol Sci 2018, 8:e1351. doi: 10.1002/wcms.1351

The sensing mechanism studies of the fluorescent probes with electronically excited state calculations

New insight into surface wetting of coal with varying coalification degree: An experimental and molecular dynamics simulation study

ReaxFF simulations of the synergistic effect mechanisms during co-pyrolysis of coal and polyethylene/polystyrene

ReaxFF simulations of hydrothermal treatment of lignite and its impact on chemical structures

A ReaxFF molecular dynamics study on the mechanism of organic sulfur transformation in the hydropyrolysis process of lignite

TDDFT study on the sensing mechanism of a fluorescent sensor for fluoride anion: Inhibition of the ESPT process.

ReaxFF and DFT study on the sulfur transformation mechanism during the oxidation process of lignite

Three-dimensional structural models for lignite and metal-ion-exchanged lignite were constructed to investigate the impact of added metal species on their pyrolysis. The Wender model was used as the structural unit of the two models, and Ca(OH)2 was used as the added metal species. Reactive force field molecular dynamics was employed to simulate the pyrolysis of the two models at 1000–2000 K over a period of 300 ps. Subsequently, cleavage pathways in the pyrolysis of the two models were determined. The characteristics observed in the simulation agree well with the known characteristics of the lignite structure. We found that the initial reactions in the pyrolysis of the two models are mainly decarboxylation and cleavage of the bridged C–O bond. These reactions were further confirmed by density functional theory calculations. Upon addition of Ca(OH)2 to lignite, the carboxyl and phenolic hydroxyl could be deprotonated. Added metal species changed the pathways for both reactions from homolytic cleavage to h...

Feng Wang

Papers

ReaxFF simulations of hydrothermal treatment of lignite and its impact on chemical structures

A ReaxFF molecular dynamics study on the mechanism of organic sulfur transformation in the hydropyrolysis process of lignite

TDDFT study on the sensing mechanism of a fluorescent sensor for fluoride anion: Inhibition of the ESPT process.

ReaxFF and DFT study on the sulfur transformation mechanism during the oxidation process of lignite

Pyrolysis Mechanism of Metal-Ion-Exchanged Lignite: A Combined Reactive Force Field and Density Functional Theory Study