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 examined the performance of natural clinoptilolite (NC) modified with two surfactants of Triton X-100 (NC-Triton) and Tween 80 (NC-Tween) on apramycin (APR) adsorption from wastewater in...

Adsorptive removal of apramycin antibiotic from aqueous solutions using Tween 80-and Triton X-100 modified clinoptilolite: experimental and fixed-bed modeling investigations.

In this study, nanostructured γ-alumina is used as an adsorbent for the removal of nickel from aqueous solutions using a fixed-bed column and batch experiments. Different parameters, including the initial nickel solution concentration, contact time, and pH were analyzed to determine their optimum values. The results showed that adsorption efficiency increased as contact time increased; optimum contact time was observed to be 150 min. The efficiency of removing metal ions from an aqueous solution increased as pH increased from 2.5 to 4.5, but decreased as pH rose higher, thus, optimum pH was determined to be 4.5. The Langmuir isotherm model showed better agreement with the experimental data than the Freundlich and Tempkin isotherm models. The maximum capacity of the adsorbent in the Langmuir equation was 78.74 mg/g. In the present study, adsorbent bed performance breakthrough curves for different adsorbent bed heights, influent flow rates, and concentrations were analyzed. The experimental data sho...

Determination of axial dispersion and overall mass transfer coefficients for Ni (II) adsorption on nanostructured γ-alumina in a fixed bed column: experimental and modeling studies

This study investigated the interaction between B12N12 nano-cluster and carboplatin complex using B3P86 functional. Two interaction modes between B12N12 nano-cluster and carboplatin complex were considered. The bonding interaction between the B12N12 nano-cluster and carboplatin complex was examined through energy decomposition analysis (EDA). Also, Shubin Liu’s energy decomposition analysis (EDA-SBL) is used to study the source of energy differences between various isomers of B12N12  ...  carboplatin complex. Charge transfer between fragments were illustrated with electrophilicity-based charge transfer (ECT) and extended charge decomposition analysis (ECDA). The quantum theory of atoms in molecules (QTAIM) analysis was applied to assess the Pt-B and Pt-N bonds within B12N12  ...  carboplatin complex.

The interaction between carboplatin anticancer drug and B 12N 12 nano-cluster: A computational investigation

In this study, we have investigated the interaction between Al12N12 nano-cluster and titanocene dichloride anticancer drug complex using B3P86 functional. Two interactions modes between Al12N12 nano-cluster and titanocene dichloride complex (TiCl2Cp2, Cp = η5-(C5H5)2) have been studied. The bonding interaction between the Al12N12 nano-cluster and anticancer drug has been examined through energy decomposition analysis (EDA). In addition, Shubin Liu’s energy decomposition analysis (EDA-SBL) has been used to study the source of energy different between various isomers of Al12N12···cp2TiCl2 complex. Charge transfer between fragments have been illustrated with electrophilicity-based charge transfer (ECT). The related molecular properties to the biological activity of these drug precursor molecules have been studied (octanol–water partition coefficient (log P), molecular volume (Vm)). The quantum theory of atoms in molecules (QTAIM) analysis has been applied to assess the Al–Cl bonds within the Al12N12···cp2TiCl2 complexes.

Quantum Chemical Study of Interaction between Titanocene Dichloride Anticancer Drug and Al12N12 Nano-Cluster

Zeolite MWW was synthesized by microwave and hydrothermal method, and used as the support on which M/TiO2 (M = Cu, Ag, and Au) was loaded via wet impregnation method. Dibenzothiophene (DBT) removal in mild conditions was studied on various catalysts: MWW, Cu/TiO2/MWW, Ag/TiO2/MWW, and Au/TiO2/MWW. Among the synthesized composites, Au/TiO2/MWW, Ag/TiO2/MWW, and Cu/TiO2/MWW had better performance. Also, the results indicated that Au/TiO2/MWW considerably outperformed MWW. Response surface methodology (RSM) with central composite design (CCD) was used to study the effects of Au/TiO2/MWW composite loading, H2O2 volume, and temperature. Finally, the optimal conditions providing the highest conversion of sulfur (99.99%) were determined as 0.24 g Au/TiO2/MWW, 0.26 mL H2O2 and temperature of 59.4°C. Based on the results, Au/TiO2/MWW composite was shown to be an efficient catalyst for oxidation of sulfur heterocycles. The results of kinetic study indicated that pseudo first-order model has a good agreement with the experimental data. The desulfurization of gas condensate was studied under optimal conditions. The desulfurization efficiency over Au/TiO2/MWW catalyst was 89.11%.

Reza Fazaeli

Papers

Adsorptive removal of apramycin antibiotic from aqueous solutions using Tween 80-and Triton X-100 modified clinoptilolite: experimental and fixed-bed modeling investigations.

Determination of axial dispersion and overall mass transfer coefficients for Ni (II) adsorption on nanostructured γ-alumina in a fixed bed column: experimental and modeling studies

The interaction between carboplatin anticancer drug and B 12N 12 nano-cluster: A computational investigation

Quantum Chemical Study of Interaction between Titanocene Dichloride Anticancer Drug and Al12N12 Nano-Cluster

Oxidative Desulfurization of Dibenzothiophene Using M/TiO 2 /MWW (M = Cu, Ag, and Au) Composite