Atom Decomposition Research Articles

Contact and frictional behavior of rough surfaces using molecular dynamics combined with fractal theory

The microcontact behavior of a copper asperity on a diamond plate was carried out using a molecular dynamics (MD) simulation with the parallel algorithms atom decomposition method. The results show that the dynamic frictional force had an oscillated behavior when the flat diamond plane slipped through the copper asperity. The contact load, contact area, dynamic frictional force, and dynamic frictional coefficient increased as the contact interference increased at a constant loading velocity. The dynamic frictional force and dynamic frictional coefficient increased as the sliding velocity increased. Furthermore, the microcontact behavior can be evaluated between a rigid smooth flat plane and a rigid smooth hemisphere to a deformable rough flat plane by combining the deformed behavior of the asperity obtained from MD results and the fractal and statistic parameters.

Competition between mono-and bimolecular reactions of artemisinin alkoxyl radicals

The competition between intramolecular and bimolecular reactions of alkoxyl radicals formed from artemisinin was theoretically analyzed. The enthalpies of these reactions were calculated. The activation energies and rate constants of reactions of intramolecular hydrogen atom transfer, decyclization, and decomposition of alkoxyl radicals of artemisinin and several its derivatives, as well as the activation energies and rate constants of reactions of these radicals with the C-H, S-H, and O-H bonds in biological substrates and their analogs were calculated by the intersecting parabolas method The fastest reactions of artemisinin alkoxyl radicals were identified. The full kinetic scheme of transformation of these radicals was proposed. Artemisinin radicals with the free valence on the carbon atom are predominantly formed due to the transformation of the artemisininoxyl radicals.

A general purpose parallel molecular dynamics simulation program

We present a general purpose parallel molecular dynamics simulation code. The code can handle NVE, NVT, and NPT ensemble molecular dynamics, Langevin dynamics, and dissipative particle dynamics. Long-range interactions are handled by using the smooth particle mesh Ewald method. The implicit solvent model using solvent-accessible surface area was also implemented. Benchmark results using molecular dynamics, Langevin dynamics, and dissipative particle dynamics are given. Program summary Title of program:MM_PAR Catalogue identifier:ADXP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADXP_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested:any UNIX machine. The code has been tested on Linux cluster and IBM p690 Operating systems or monitors under which the program has been tested:Linux, AIX Programming language used:C Memory required to execute with typical data:∼60 MB for a system of ∼ 24 000 atoms Has the code been vectorized or parallelized? parallelized with MPI using atom decomposition and domain decomposition No. of lines in distributed program, including test data, etc.:171 427 No. of bytes in distributed program, including test data, etc.:4 558 773 Distribution format:tar.gz External routines/libraries used:FFTW free software ( http://www.fftw.org) Nature of physical problem:Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Method of solution:Molecular dynamics simulation in NVE, NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Typical running time:Table below shows the typical run times for the four test programs. Benchmark results. The values in the parenthesis are the number of processors used System Method Timing for 100 steps in seconds 256 TIP3P MD 23.8 (1) 64 DMPC + 1645 TIP3P MD 890 (1) 528 (2) 326 (4) 209 (8) 8 A β 16 – 22 LD 1.02 (1) 23760 Groot–Warren particles DPD 22.16 (1)

Parallel short range molecular dynamics simulations on computer clusters: Performance evaluation and modeling

This paper describes the performance of a portable molecular dynamics code running on an eight-node PC cluster. The molecular dynamics code is based on the atom decomposition method for distributing the computation load among the processors and the MPI protocol for managing communications among processors. We discuss the changes made to the serial code with an effort to maintain its readability. We examined the program performance for system sizes of order 10 2 to 10 4 atoms and number of processors varying from 1 to 8, by measuring the total execution time and the corresponding speedup, as well as the communication time for data exchange and the time for the calculation of interatomic forces. Using simple communication and computation load considerations, we propose models in order to explain the observed behaviour and predict the optimal usage of the cluster. It turns out that using few parameters that can be easily measured one can predict quite accurately the optimal usage of small clusters running short range molecular dynamics programs.

Approximation of Hardy space on the unit sphere

The authors discuss the boundedness and approximation properties of translation and mean operator on H 1 ( Σ ) by the estimates of high degree difference on ultraspherical polynomials, atom decomposition and construct properties on sphere. Also the boundedness and approximation of linear means at all kinds of indexes on H p (0 p < 1) and the almost everywhere convergence of Cesaro means are established.

Weighted Hardy spaces on homogeneous groups

This paper is devoted to study the atom decomposition of the weighted Hardy space on a homogeneous group X. Some results are extensions of the objects studied in Euclidean harmonic analysis.

Tetraorganoammonium polydimethylsiloxanolates

A number of α,ω-bis-tetraorganoammonium dimethylsiloxanolates, of the type R 4N—[OSiMe 2] n ONR 4, where R 4 = Me 4; Et 4; n-Bu 4; PhCH 2, Me 3, Ph, Me 2, Et; Ph, Me 2, n-Bu; has been synthesized. The thermal stability of the siloxanolates has been studied and for decomposition of these compounds the order of reaction has been determined, and the rate constants and energies of activation calculated. Analysis of the decomposition products showed that if the organic radical contains an H atom in the β-position with respect to the nitrogen atom decomposition occurs by elimination of an olefinic hydrocarbon and water, and formation of a siloxane bond. In decomposition of siloxanolates that do not contain H atoms in the β-position with respect to N a terminal alkoxyl group is formed and an amine is liberated.