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

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

We show that the Raman scattering technique can give complete structural information for one-dimensional systems, such as carbon nanotubes. Resonant confocal micro-Raman spectroscopy of an (n,m) individual single-wall nanotube makes it possible to assign its chirality uniquely by measuring one radial breathing mode frequency omega(RBM) and using the theory of resonant transitions. A unique chirality assignment can be made for both metallic and semiconducting nanotubes of diameter d(t), using the parameters gamma(0) = 2.9 eV and omega(RBM) = 248/d(t). For example, the strong RBM intensity observed at 156 cm(-1) for 785 nm laser excitation is assigned to the (13,10) metallic chiral nanotube on a Si/SiO2 surface.

Structural (n,m) determination of isolated single wall carbon nanotubes by resonant Raman scattering

Poly(vinylidene fluoride) (PVDF) has excellent pyro- and piezoelectric properties which are related to the β-crystal of PVDF. Most of the β-crystal of PVDF can be transformed from the α-crystal by mechanical stretching. The effects of stretching conditions on the transformation from α to β phase of PVDF were studied in this paper. In addition, changes of crystalline structure of PVDF during the stretching process were observed in situ under an optical tensile stress microscopy tester, and the samples after being stretched were investigated using a 3D digital microscope and an infrared microscope. The results show that stretching temperature (Ts) and drawing ratio (λ) are critical to the transformation from α-crystal to β-crystal of PVDF. The Ts around 100 °C and λ above 3 is recommended. The in situ observation indicates that the deformation of crystalline structure began from the middle of α-spherulite and extended to another spherulite, and caused the large-scale transformation. Scanning results of infrared microspectroscopic and 3D digital microscopy revealed that α phase of PVDF would change into β phase with the deformation of the spherulite, and the distribution of the different crystalline phase in PVDF after being stretched was also given. It is believed that this work is instructive and meaningful to studies on phase transformation and production of the piezoelectric film of PVDF.

Studies on the transformation process of PVDF from α to β phase by stretching

Catalytic hydrogenation of CO2 with renewable H2 to methanol represents a promising pathway for reducing anthropogenic CO2 emissions. Catalysts play a key role in enhancing both the hydrogenation r...

CO2 Hydrogenation to Methanol over ZrO2-Containing Catalysts: Insights into ZrO2 Induced Synergy

Simulation of α- and β-PVDF melting mechanisms

Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase

http://hb.diva-portal.org/smash/get/diva2:869627/FULLTEXT01

Molecular modelling of oxygen and water permeation in polyethylene

http://liu.diva-portal.org/smash/get/diva2:1197953/FULLTEXT01

Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts

Porphobilinogen synthase (PBGS) is a key enzyme in heme biosynthesis that catalyzes the formation of porphobilinogen (PBG) from two 5-aminolevulinic acid (5-ALA) molecules via formation of intersub ...

/pdf/computational-insights-into-the-mechanism-of-porphobilinogen-irw6rpueuw.pdf

Edvin Erdtman

Papers

Simulation of α- and β-PVDF melting mechanisms

Computational studies on Schiff-base formation : Implications for the catalytic mechanism of porphobilinogen synthase

Molecular modelling of oxygen and water permeation in polyethylene

Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts

Computational insights into the mechanism of porphobilinogen synthase.