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

1. Introduction 46372. Theoretical Methodologies and Simulation Tools 46402.1. Ab Initio Quantum Chemistry 46412.2. Molecular Dynamics 46422.2.1. Classical Molecular Dynamics and MonteCarlo Simulations46432.2.2. Empirical Valence Bond Models 46442.2.3. Ab Initio Molecular Dynamics (AIMD) 46452.3. Poisson−Boltzmann Theory 46452.4. Nonequilibrium Statistical Mechanical IonTransport Modeling46462.5. Dielectric Saturation 46473. Transport Mechanisms 46483.1. Proton Conduction Mechanisms 46483.1.1. Homogeneous Media 46483.1.2. Heterogeneous Systems (ConfinementEffects)46553.2. Mechanisms of Parasitic Transport 46613.2.1. Solvated Acidic Polymers 46613.2.2. Oxides 46654. Phenomenology of Transport inProton-Conducting Materials for Fuel-CellApplications46664.1. Hydrated Acidic Polymers 46664.2. PBI−H

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Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology.

: 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 review some recently published methods to represent atomic neighborhood environments, and analyze their relative merits in terms of their faithfulness and suitability for fitting potential energy surfaces. The crucial properties that such representations (sometimes called descriptors) must have are differentiability with respect to moving the atoms and invariance to the basic symmetries of physics: rotation, reflection, translation, and permutation of atoms of the same species. We demonstrate that certain widely used descriptors that initially look quite different are specific cases of a general approach, in which a finite set of basis functions with increasing angular wave numbers are used to expand the atomic neighborhood density function. Using the example system of small clusters, we quantitatively show that this expansion needs to be carried to higher and higher wave numbers as the number of neighbors increases in order to obtain a faithful representation, and that variants of the descriptors converge at very different rates. We also propose an altogether different approach, called Smooth Overlap of Atomic Positions, that sidesteps these difficulties by directly defining the similarity between any two neighborhood environments, and show that it is still closely connected to the invariant descriptors. We test the performance of the various representations by fitting models to the potential energy surface of small silicon clusters and the bulk crystal.

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On representing chemical environments

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

The interaction of high energy radiation (� , � , � rays or heavy ions) with living cells does not in general directly lead to DNA strand breaks. The primary interaction essentially removes electrons from the components of the complex molecular network, i.e., electrons from valence states of the chemical bonds but also electrons from localized inner shells of the individual atoms. As a result of the subsequent charge transfer and energy dissipating processes, chemical bonds can be ruptured generating neutral or ionic radicals as additional secondary species. Electrons as the most abundant secondary species are created with an estimated quantity of � 4 � 10 4 electrons per MeV primary quantum deposited [1]. The larger majority possesses initial kinetic energies up to about 20 eV [2]. In the course of successive inelastic collisions within the medium they are thermalized within 10 � 12 s before they reach some stage of solvation, then as chemical rather inactive species. Moreover, damage of the genom in a living cell by ionizing radiation is about one-third direct and two-thirds indirect [3]. Direct damage concerns reactions directly in the DNA and its closely bound water molecules and indirect damage results from energy deposition in water molecules and other biomolecules in the surrounding of the DNA. It is believed that almost all the indirect damage is due to the attack of the highly reactive hydroxyl radical [4,5]. The importance of reactions of presolvated electrons with amino acids and nucleotides has already been pointed out more than two decades ago by time resolved pulse radiolysis experiments [6]. More recently, the ability of free ballistic electrons (3‐20 eV) to efficiently induce single and double strand breaks in supercoiled DNA has clearly been shown by Sanche and co-workers [7]. In these studies it was demonstrated that the DNA strand breaks were initiated by the formation and decay of transient negative ion (TNI) states, localized on the various DNA components (base, phosphate, deoxyribose, or hydration water). Resonances in DNA strand break curves were observed in the energy range around 10 eV ,s imilar to those TNI states formed by these components in the gas phase or in homogeneous films as exemplified in Ref. [7]

/pdf/electron-attachment-to-uracil-effective-destruction-at-3npfuey7fa.pdf

Electron attachment to uracil: effective destruction at subexcitation energies.

Proton transfer reaction - mass spectrometry (PTR-MS) has become a reference technique in environmental science allowing for VOC monitoring with low detection limits. The recent introduction of time-of-flight mass analyzer (PTR-ToF-MS) opens new horizons in terms of mass resolution, acquisition time, and mass range. A standard procedure to perform quantitative VOC measurements with PTR-ToF-MS is to calibrate the instrument using a standard gas. However, given the number of compounds that can be simultaneously monitored by PTR-ToF-MS, such a procedure could become impractical, especially when standards are not readily available. In the present work we show that, under particular conditions, VOC concentration determinations based only on theoretical predictions yield good accuracy. We investigate a range of humidity and operating conditions and show that theoretical VOC concentration estimations are accurate when the effect of water cluster ions is negligible. We also show that PTR-ToF-MS can successfully be used to estimate reaction rate coefficients between H(3)O(+) and VOC at PTR-MS working conditions and find good agreement with the corresponding nonthermal theoretical predictions. We provide a tabulation of theoretical rate coefficients for a number of relevant volatile organic compounds at various energetic conditions and test the approach in a laboratory study investigating the oxidation of alpha-pinene.

On Quantitative Determination of Volatile Organic Compound Concentrations Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry

We present a detailed study on dissociative electron attachment (DEA) to isolated gas-phase cytosine (C) and thymine (T). The experimental setup used for these measurements is a crossed electron/neutral beam instrument combined with a quadrupole mass spectrometer. Electron attachment to these biomolecules leads to dissociation into various fragments without a hint of any measurable amount of stable C or T parent anions. The fragment anions with highest abundance are (C−H)- and (T−H)-, respectively. Quantum chemical calculations were performed to calculate the electron affinities and binding energies of the different isomers of the (T−H) fragment. Besides (C−H)- and (T−H)-, we observed five other fragment anions formed by DEA to cytosine and eight additional product anions were detected in the case of thymine. Ion efficiency curves were measured for all fragment anions in the electron energy range from about 0 to 14 eV. For mixtures of T or C with SF6 or CCl4 in the collision chamber, additional resonances...

Michael Probst

Papers

Electron attachment to uracil: effective destruction at subexcitation energies.

On Quantitative Determination of Volatile Organic Compound Concentrations Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry

Electron Attachment to the Gas-Phase DNA Bases Cytosine and Thymine

Molecular dynamics and x-ray investigation of an aqueous calcium chloride solution

Contact ion pair formation and ether oxygen coordination in the polymer electrolytes M[N(CF3SO2)2]2PEOn for M = Mg, Ca, Sr and Ba