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

Theoretical studies of the oxidative addition of PhBr to Pd(PX3)2 and Pd(X2PCH2CH2PX2) (X = Me, H, Cl)

The effects of suspending Copper nanoparticles into Argon base fluid inside a microchannel under boiling flow condition by using of molecular dynamic simulation

Ultrasound assisted emulsification of solidified floating organic drop microextraction (USAE-SFODME), combined with electrothermal atomic absorption spectrometry (ETAAS), was developed for the preconcentration and determination of trace amounts of As(III) and As(V) in environmental water samples. At pH = 1, As(III) formed complexes with ammonium pyrrolidine dithiocarbamate (APDC) and these were extracted into the fine droplets of 1-dodecanol (extraction solvent) which were dispersed with the aid of ultrasonication into the water sample solution. After extraction, the organic phase was separated by centrifugation, and was solidified by transferring into an ice bath. The solidified solvent was transferred to a vial and melted quickly at room temperature. As(III) was determined in the melted organic phase while As(V) remained in the aqueous layer. Total inorganic As was determined after the reduction of the pentavalent forms of arsenic with sodium thiosulphate and potassium iodide. The concentration of As(V) was calculated as the difference between the concentrations of total inorganic As and As(III). The variables of interest in the USAE-SFODME method, such as the volume of extraction solvent, pH, concentration of APDC (chelating agent), sonication time and salt effect were optimized using multivariate optimization approaches. A fractional factorial design (FFD) for screening and a central composite design for optimizing the significant variables were applied. A mathematical model was presented that successfully predicts changes in the response, depending on the input variables. Under the optimum conditions, the proposed method has been successfully used for the determination of inorganic arsenic in different environmental water samples and certified reference material (NIST RSM 1643e).

Application of multi-factorial experimental design to successfully model and optimize inorganic arsenic speciation in environmental water samples by ultrasound assisted emulsification of solidified floating organic drop microextraction

Background: The trace element copper has been identified as a highly toxic element for sperm. It is known to affect sperm motility in humans, and experimental implantation of copper in the epididymis, vas deferens, and scrotum of mammals has been demonstrated to affect fertility detrimentally. Objective: Sperm concentration, motility, vitality and morphology are parameters used to evaluate potential male fertility. Since, copper is believed to be important for spermatogenesis; we conducted a study to investigate the correlation between seminal plasma copper concentration and human semen parameters in 232 males. Materials and Methods: We selected 232 subfertile or infertile men who referred to Omid Fertility Clinic, randomly. Samples were categorized into normospermic (n=32), oligozospermic (n=73), asthenozospermic (n=111) and azospermic (n=16) groups according to their spermiogrames. Total seminal plasma copper concentration was determined by furnace atomic absorption spectrophotometer. Results: The results showed that seminal plasma copper concentrations in oligozospermic, asthenozospermic and azospermic groups are significantly higher than normozospermic group (p<0.01). Also, negative correlations were found between seminal plasma copper concentration and sperm count (p<0.05), sperm motility (p<0.01), sperm vitality (p<0.01), normal morphology (p<0.01) and pH (p<0.01) in all groups. Conclusion: It was suggested that excess copper in seminal plasma was detrimental for male reproductive capacity by reducing sperm count, motility, vitality and morphology.

/pdf/seminal-plasma-levels-of-copper-and-its-relationship-with-2mcc0i7t3g.pdf

Seminal plasma levels of copper and its relationship with seminal parameters

This paper presents molecular dynamics simulations to study on the effects of external driving force and boundary wall temperature on the density, velocity and temperature profiles of Argon fluid atoms, flowed in a platinum microchannel with square section. The Argon atoms are structured in three regions. Two thin liquid film of Argon sandwich central vapor zone. Applying wall temperatures in the range of 84K to 133K prepares boiling condition which causes liquid atoms move from lateral layers to central bins of microchannel. Afterward, density of central layers of microchannel increases which is highlighted by sampling data after equilibrium condition of system energy in 4 time steps. It is concluded that augmentation of external driving forces on the Argon atoms from 0.002 to 0.01 and 0.02 eV/Angstrom can increase flow temperature from 180K to 1920K and 7570K, respectively which is noticeable for practical application such as medical especially in Cryosurgery. Moreover, augmentation of external forces can increase velocity profiles of Argon fluid flow. Generally, density was independent from variation of external force and boundary wall temperature in the studied limits. Also, alteration of boundary wall temperature does not play very important role on the velocity and temperature of Argon fluid inside microchannel.

Reza Fazaeli

Papers

Theoretical studies of the oxidative addition of PhBr to Pd(PX3)2 and Pd(X2PCH2CH2PX2) (X = Me, H, Cl)

The effects of suspending Copper nanoparticles into Argon base fluid inside a microchannel under boiling flow condition by using of molecular dynamic simulation

Application of multi-factorial experimental design to successfully model and optimize inorganic arsenic speciation in environmental water samples by ultrasound assisted emulsification of solidified floating organic drop microextraction

Seminal plasma levels of copper and its relationship with seminal parameters

A statistical method for simulation of boiling flow inside a Platinum microchannel