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

Study of the microscopic mechanism of lauryl glucoside wetting coal dust: Environmental pollution prevention and control.

Polycyclic aromatic hydrocarbons (PAHs) are frequently detected in soil. Their biological toxicity and carcinogenic, teratogenic, and mutagenic effects pose a great threat to the ecological environment and human health. Firstly, the sources, physicochemical properties, and environmental hazards of PAHs are reviewed in this paper, and then their pollution status and different methods for their detection in soil are described in detail. The remediation technologies to treat pollution in the field and farmland are compared, and the technical status and factors influencing phytomicrobial remediation of PAHs in contaminated soil are evaluated in the most comprehensive way. The mechanisms of phytomicrobial remediation of PAHs-contaminated soil under different conditions are innovatively discussed. Additionally, the regulation mechanism of enzymes involved in plant and microbial degradation of PAHs in soils is studied. This is the first study on the regulation mechanism of degradation enzyme in a PAHs review. The aim of this paper is to review the pollution status, remediation technologies, mechanisms, and biodegradation actions of PAHs in soil. This review creatively provides reliable technical support for strengthening soil remediation and environmental management.

Analysis of Factors Influencing Plant–Microbe Combined Remediation of Soil Contaminated by Polycyclic Aromatic Hydrocarbons

Background Knowledge of the stabilizing mechanisms of soil organic matter (SOM) is extremely important for numerous soil functions. For this, insight into the nature of organic matter through appropriate model concepts are crucial. Aims For several years, a heated debate has emerged on the transformation and stabilization of SOM. In the present work, we try to contribute to this debate using molecular modeling and providing a comprehensive overview of the history of application of molecular modeling tools and developing structural concepts of SOM. Methods Molecular modeling methods based on quantum and/or classical mechanics were used to model SOM and related properties including interactions with reactive surfaces of soil minerals. Results Modeling of SOM aggregates revealed that hydrogen bonds and cation bridges are the main stabilizing factors in soil solution, whereas pH modifies the stability. The modeled supramolecular SOM aggregates exhibit physicochemical properties, similar to those of humic substances (HS) described in literature. The interactions of the HS models with surfaces in kaolinite nanopores led to a partial disintegration of the aggregates into individual molecules and/or smaller subaggregates. Conclusions From the molecular modeling point of view, supramolecular microaggregate models that exhibit the properties of HS are stable in the soil solution. However, their binding to reactive mineral soil constituents can be also in the form of individual molecules or subaggregates. Thus, HS microaggregate stability is relative, depending on the interacting environment. This reconciles two points of view of HS: either as small molecules and/or supramolecular structures. 

A contribution of molecular modeling to supramolecular structures in soil organic matter
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A simple empirical model for phenanthrene adsorption on soil clay minerals

Humic acid (HA) and water play an important role in polycyclic aromatic hydrocarbons (PAHs) adsorption and biodegradation in soil. In this work, molecular dynamics (MD) and electrostatic potential surfaces (EPSs) simulations are conducted to research the contribution of quartz surface, leonardite humic acid (LHA), and water to PAH adsorption. The adsorption energies between PAHs and LHA are much higher than that between PAHs and quartz. Simulation shows that the hydroxyl and carboxyl groups’ attraction by LHA is the main adsorption force between PAHs and LHA. The π-π interaction between PAHs and LHA also contributes to the adsorption process. In addition, the mobility of water on quartz surface is much higher than that of LHA. Water should be regarded as an adsorbate in the system as well as PAHs. However, the presence of water has a remarkable negative effect on the adsorption of PAHs on LHA and quartz. The bridging effect of water could only enhance the stability of the aggregation system. The adsorption contribution of quartz and LHA to PAHs in the soil model tends to 0 if the water layer reaches 2.0 nm.

Nan Zhao

Papers

Molecular dynamics simulation of the interaction of water and humic acid in the adsorption of polycyclic aromatic hydrocarbons

A simple empirical model for phenanthrene adsorption on soil clay minerals