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

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Density functional theory for transition metals and transition metal chemistry

Guidelines for the use and interpretation of adsorption isotherm models: A review.

Adsorption kinetic models: Physical meanings, applications, and solving methods.

Adsorption isotherm models: Classification, physical meaning, application and solving method

This study was conducted to synthesize copper(II) oxides (CuO) with dendrite, leaf and feather morphologies. Synthesized CuO with dendrite and leaf morphologies were characterized by XRD, SEM, and BET/BJH and CuO with feather morphology with XRD, SEM, BET/BJH, FTIR, TEM, and DRS techniques. The effect of various CuO morphologies on Zn(II) adsorption was investigated. Among the morphologies observed in all experiments, feather morphology showed the highest efficiency. In order to evaluate the parameters X1 (mass of adsorbent (CuO feather)), X2(pH) and X3 (contact time) in Zn(II) adsorption, the design of the experiment was performed using the Box–Behnken Design (BBD) method. Finally, the optimum conditions, mass of adsorbent (0.14 g), pH (7.99), and contact time (44.78 h) the Zn(II) adsorption efficiency was 99.98%. In the kinetic study of the reaction, it was also found that the adsorption process follows a pseudo-second order kinetic model.

Investigation of Zn(II) Adsorption from Aqueous Solution onto Copper Oxide with Different Morphologies: Optimization Using Response Surface Methodology

In this study, natural bond orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have been used to illustrate structure and bonding in iron aminoborirene complex [(η5-C5H5)(OC)2Fe{μ-BN(SiH3)2C=C}Ph] (closed-isomer) and its isomer boryl complex [(η5-C5H5)(OC)2FeBN(SiH3)2C≡CPh] (open-isomer). It has been found that the closed isomer has minor stability as compared to the open isomer. Natural bond orbital analysis (NBO), Quantum theory of atoms in molecules analysis (QTAIM), Electron localization function (ELF), and Localized orbital locator (LOL) analyses have been applied to assess the Fe-C and F-B bonds in the complexes.

Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) Analyses of Iron-Substituted Borirene and Boryl Isomers

The aim of this study was to evaluate the efficiency of NiO/WO3 heterostructure photocatalytic process for removal of lincomycin antibiotic from aqueous solutions. WO3, NiO, and NiO/WO3 particles were synthesized and characterized by several techniques. NiO and WO3 photocatalytic properties in removal of lincomycin antibiotic were evaluated from experimental and theoretical perspectives. The influence of various parameters such as type of irradiation and photocatalyst, initial concentration of lincomycin (mg/L), NiO loading percentage (wt %), mass of NiO/WO3 (g), time (h), and pH were investigated. According to the results, the interaction energy for lincomycin adsorbed on NiO surface was –114.717 kJ mol–1 and for adsorbed on WO3 surface was –28.379 kJ mol–1. It is apparent from these interaction energy values that lincomycin adsorbed on WO3 surface has more negative Eint values and stronger interactions as compared to NiO surface. According to the experimental and theoretical results, loading of NiO onto WO3 increased the catalyst adsorption to lincomycin and ultimately increased the removal efficiency. The results shown that pH plays an important role in the removal of lincomycin. The maximum removal efficiency of 98.56% was obtained at pH 5, 0.2 g NiO/WO3 (2 wt %), 25 mg/L initial lincomycin concentration and 2 h exposure under sunlight.

Preparation of NiO/WO3 Heterostructure and Photocatalytic Properties in Removal of Lincomycin Antibiotic: Experimental Study and Molecular Dynamic Simulation

Comparative study of the of azo Dyes (as a class important organic pollutants photodegradation process) in aqueous solution employing H2 O2 /UV and K2 S2 O8 /UV systems in a photochemical reactor were investigated. Lead zirconate titanate [Pb (Zr0.58Ti0.42) O3 ] (PZT) nanocatalyst was synthesized via the sol-gel method. Then, photocatalytic properties of dopant type on PZT were determined in a UV photoreactor in the presence of different radical generators. These comparative studies showed that PZT/TiO2 and PZT/TiO2 /FeCl3 have higher efficiency than the others.

http://jacr.kiau.ac.ir/article_516257_5ba378a872b3572a8d16470050971426.pdf

Environmental Remediation of Organic Pollutants in Synthesized and Characterized Aqueous Suspension by Photochemical Method: A Kinetic Study

In this study, nanostructured γ-alumina has been used as an adsorbent for nickel removal from aqueous solution in a fixed-bed column. Comparison of Thomas, Yoon-Nelson, and Adams-Bohart models with the experimental kinetic results was done and model parameters were evaluated using a linear regression analysis for Ni2+ adsorption in different bed heights, initial concentrations, and flow rates. The obtained experimental data was in good agreement with Thomas and Yoon-Nelson models, but in the case of Adams-Bohart model, a low correlation coefficient was observed.

Reza Fazaeli

Papers

Investigation of Zn(II) Adsorption from Aqueous Solution onto Copper Oxide with Different Morphologies: Optimization Using Response Surface Methodology

Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) Analyses of Iron-Substituted Borirene and Boryl Isomers

Preparation of NiO/WO3 Heterostructure and Photocatalytic Properties in Removal of Lincomycin Antibiotic: Experimental Study and Molecular Dynamic Simulation

Environmental Remediation of Organic Pollutants in Synthesized and Characterized Aqueous Suspension by Photochemical Method: A Kinetic Study

Continuous Flow Separation of Ni(II) from Aqueous Solution by Nanostructured γ-Alumina