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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

A second-generation potential energy function for solid carbon and hydrocarbon molecules that is based on an empirical bond order formalism is presented. This potential allows for covalent bond breaking and forming with associated changes in atomic hybridization within a classical potential, producing a powerful method for modelling complex chemistry in large many-atom systems. This revised potential contains improved analytic functions and an extended database relative to an earlier version (Brenner D W 1990 Phys. Rev. B 42 9458). These lead to a significantly better description of bond energies, lengths, and force constants for hydrocarbon molecules, as well as elastic properties, interstitial defect energies, and surface energies for diamond.

/pdf/a-second-generation-reactive-empirical-bond-order-rebo-3nq9vxvup4.pdf

A second-generation reactive empirical bond order (REBO) potential energy expression for hydrocarbons

https://is.muni.cz/el/1431/podzim2006/C7780/um/Read/2711172/SAM_str_grwth_ProgSurfSci00_151.pdf

Structure and growth of self-assembling monolayers

Author(s): Vogel, Alfred; Venugopalan, Vasan | Abstract: The mechanisms of pulsed laser ablation of biological tissues were studied. The transiently empty space created between the fiber tip and the tissue surface improved the optical transmission to the target and thus increased the ablation efficiency. It was found that the structure and morphology also affect the energy transport among tissue constituents.

/pdf/mechanisms-of-pulsed-laser-ablation-of-biological-tissues-58cltfa63z.pdf

Mechanisms of pulsed laser ablation of biological tissues.

The results of large-scale molecular dynamics simulations demonstrate that the mechanisms responsible for material ejection as well as most of the parameters of the ejection process have a strong dependence on the rate of the laser energy deposition. For longer laser pulses, in the regime of thermal confinement, a phase explosion of the overheated material is responsible for the collective material ejection at laser fluences above the ablation threshold. This phase explosion leads to a homogeneous decomposition of the expanding plume into a mixture of liquid droplets and gas phase molecules. The decomposition proceeds through the formation of a transient structure of interconnected liquid clusters and individual molecules and leads to the fast cooling of the ejected plume. For shorter laser pulses, in the regime of stress confinement, a lower threshold fluence for the onset of ablation is observed and attributed to photomechanical effects driven by the relaxation of the laser-induced pressure. Larger and more numerous clusters with higher ejection velocities are produced in the regime of stress confinement as compared to the regime of thermal confinement. For monomer molecules, the ejection in the stress confinement regime results in broader velocity distributions in the direction normal to the irradiated surface, higher maximum velocities, and stronger forward peaking of the angular distributions. The acoustic waves propagating from the absorption region are much stronger in the regime of stress confinement and the wave profiles can be related to the ejection mechanisms.

Microscopic mechanisms of laser ablation of organic solids in the thermal and stress confinement irradiation regimes

ion reactions by primary radicals, for example: C6H5Cl + •Cl f C6H4Cl• + HCl ∆H°rxn ) from -109.3 to -66.4 kJ/mol Radical-radical recombination reactions, for example: Cl• + •Cl f Cl2 ∆H°rxn ) -239.2 kJ/mol C6H5• + •C6H5 f C12H10 ∆H°rxn ) -564.4 to -478.9 kJ/mol Computer Simulations of Laser Ablation of Molecular Substrates Chemical Reviews, 2003, Vol. 103, No. 2 327

Computer Simulations of Laser Ablation of Molecular Substrates

Irradiation of organic polymers by short pulses of far‐UV (e.g., 193 nm) laser light causes ablative photodecomposition (APD) of the material. This etching process occurs cleanly leaving behind a well‐defined pit. Longer wavelength (e.g., 532 nm) laser light also ablates material from a polymeric solid. However, this process is distinct from APD in that the sample near the pit is distorted and melted. Microscopic models are presented here for both the photochemical and thermal processes. The photochemical model predicts that well‐defined pits will be formed, that narrow angular distributions of the ablated material should be observed, and that the average perpendicular ejection velocity will be 1000–2000 m/s. The thermal model predicts melting or distortion of the solid and a broad angular distribution of the ejected material.

Laser ablation of organic polymers: Microscopic models for photochemical and thermal processes

A breathing sphere model is developed for molecular dynamics simulations of laser ablation and desorption of organic solids. An approximate representation of the internal molecular motion permits a significant expansion of the time and length scales of the model and still allows one to reproduce a realistic rate of the vibrational relaxation of excited molecules. We find that the model provides a plausible description of the ablation of molecular films and matrix-assisted laser desorption. An apparent threshold fluence has been found to separate two mechanisms for the ejection of molecules: surface vaporization at low laser fluences and collective ejection or ablation at high fluences. Above threshold the laser-induced high pressure and the explosive homogeneous phase transition lead to the strongly forwarded emission of ablated material and high, from 500 up to 1500 m/s, maximum velocities of the ejected plume expansion. Large analyte molecules get axial acceleration from an expanding plume and move along with the matrix molecules at nearly the same velocities. Big molecular clusters are found to constitute a significant part of the ejected plume at fluences right above the ablation threshold. The processes in the plume are found to have a strong influence on the final velocities of ejected molecules and molecular clusters.

Molecular dynamics model for laser ablation and desorption of organic solids

Computer simulations of hydrocarbon and related molecules using empirical force fields have become important tools for studying a number of biological and related processes at the atomic scale. Traditional force fields, however, cannot be used to simulate dynamic chemical reactivity that involves changes in atomic hybridization. Application of a many-body potential function allows such reactivity to occur in a computer simulation. Simulations of the reaction of small hydrocarbon molecules adsorbed on a reconstructed diamond {001}(2x1) surface suggest that these hydrocarbons are highly reactive species and that initial stages of diamond growth proceed through a dimer-opening mechanism. Rates estimated from transition state theory of two interconversions between states where the dimer is open and closed are given.

https://science.sciencemag.org/content/sci/255/5046/835.full.pdf

Barbara J. Garrison

Papers

Microscopic mechanisms of laser ablation of organic solids in the thermal and stress confinement irradiation regimes

Computer Simulations of Laser Ablation of Molecular Substrates

Laser ablation of organic polymers: Microscopic models for photochemical and thermal processes

Molecular dynamics model for laser ablation and desorption of organic solids

Molecular Dynamics Simulations of Dimer Opening on a Diamond {001}(2x1) Surface