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

Intermolecular And Surface Forces

Fundamentals and advances in magnesium alloy corrosion

The anomalous properties of cold and supercooled water, such as the fact that at sufficiently low temperatures it becomes more compressible and less dense when cooled, and more fluid when compressed, have attracted the attention of physical scientists for a long time. The discovery in the 1970s that several thermodynamic and transport properties of supercooled water exhibit a pronounced temperature dependence and appear to diverge slightly below the homogeneous nucleation temperature inspired a large number of experimental and theoretical studies. Likewise, an important body of work on glassy water has been stimulated by experiments, starting in the mid-1980s and continuing to this date, which suggest that vitreous water can exist in at least two apparently distinct forms. A coherent theory of the thermodynamic and transport properties of supercooled and glassy water does not yet exist. Nevertheless, significant progress towards this goal has been made during the past 20 years. This article summarizes the known experimental facts and reviews critically theoretical and computational work aimed at interpreting the observations and providing a unified viewpoint on cold, non-crystalline, metastable states of water.

https://iopscience.iop.org/article/10.1088/0953-8984/15/45/R01/pdf

Supercooled and glassy water

Production of plant secondary metabolites: a historical perspective

Summary In vitro cultures are being considered as an alternative to agricultural processes for producing valuable secondary metabolites. Most efforts that use differentiated cultures instead of cell suspension cultures have focused on transformed (hairy) roots. Bioreactors used to culture hairy roots can be roughly divided into three types: liquid-phase, gas-phase, or hybrid reactors that are a combination of both. The growth and productivity of hairy root cultures are reviewed with an emphasis on successful bioreactors and important culture considerations. The latter include strain selection, production of product in relation to growth phase, media composition, the gas regime, use of elicitors, the role of light, and apparent product loss. Together with genetic engineering and process optimization, proper reactor design plays a key role in the development of successful large-scale production of secondary metabolites from plant cultures.

Invited review: secondary metabolism of hairy root cultures in bioreactors

In vitro cultures are being considered as an alternative to agricultural processes for producing valuable secondary metabolites. Most efforts that use differentiated cultures instead of cell suspension cultures have focused on transformed (hairy) roots. Bioreactors used to culture hairy roots can be roughly divided into three types: liquid-phase, gas-phase, or hybrid reactors that are a combination of both. The growth and productivity of hairy root cultures are reviewed with an emphasis on successful bioreactors and important culture considerations. The latter include strain selection, production of product in relation to growth phase, media composition, the gas regime, use of elicitors, the role of light, and apparent product loss. Together with genetic engineering and process optimization, proper reactor design plays a key role in the development of successful large scale production of secondary metabolites from plant cultures.

Secondary metabolism of hairy root cultures in bioreactors

We report homogeneous ice nucleation rates between 202 K and 215 K, thereby reducing the measurement gap that previously existed between 203 K and 228 K. These temperatures are significantly below the homogenous freezing limit, TH ≈ 235 K for bulk water, and well within no-man's land. The ice nucleation rates are determined by characterizing nanodroplets with radii between 3.2 and 5.8 nm produced in a supersonic nozzle using three techniques: (1) pressure trace measurements to determine the properties of the flow as well as the temperature and velocity of the droplets, (2) small angle X-ray scattering (SAXS) to measure the size and number density of the droplets, and (3) Fourier Transform Infrared (FTIR) spectroscopy to follow the liquid to solid phase transition. Assuming that nucleation occurs throughout the droplet volume, the measured ice nucleation rates Jice,V are on the order of 1023 cm−3 s−1, and agree well with published values near 203 K.

Freezing water in no-man's land

This work presents a systematic investigation of binary nucleation rates for sulfuric acid and water and the effect of temperature on these rates at isothermal, subsaturated conditions. The results from nucleation rate measurements for the sulfuric acid (H2SO4)–water system are discussed and compared to those previously presented for methanesulfonic acid (MSA)–water [B. E. Wyslouzil, J. H. Seinfeld, R. C. Flagan, and K. Okuyama, J. Chem. Phys. (submitted)]. Experiments were conducted at relative humidities (Rh) ranging from 0.006<Rh<0.65, relative acidities (Ra) in the range of 0.04<Ra<0.46, and at three temperatures, T=20, 25, and 30 °C, in the continuous flow mixing-type apparatus described in Paper I. Particles were formed by binary nucleation and grew by condensation as the mixed stream flowed through an isothermal glass tube. Number concentrations observed at the exit of the nucleation and growth tube as a function of Rh and Ra are extremely sensitive to the binary nucleation rate, and from these data the nucleation rate was estimated as a function of saturation level and temperature. Particle size distributions were also measured using a specially constructed differential mobility analyzer. As anticipated, the H2SO4 particles formed by nucleation and growth are much smaller than those formed in the MSA–water experiments, but particle size distribution measurements confirm that most of the particles formed are being observed. The ratio of experimental to theoretical nucleation rates, Jexpt/Jtheor, was found to be a strong function of the predicted number of acid molecules in the critical nucleus for both the H2SO4–water and MSA–water systems.

/pdf/binary-nucleation-in-acid-water-systems-ii-sulfuric-acid-3vvukuh5fc.pdf

Binary nucleation in acid–water systems. II. Sulfuric acid–water and a comparison with methanesulfonic acid–water

Very recently, Wolk and Strey [J. Phys. Chem. B 105, 11683 (2001)] presented empirical temperature correction functions for calculating homogeneous nucleation rates J of H2O and D2O (1<J/cm−3 s−1<1020) from classical nucleation theory over an extended range of temperature T (200<T/K<310) and supersaturations S (5<S<200). Here, we critically test the correction functions to the Becker–Doring nucleation rate equation JBD against an extensive set of experimental data, and find that the equations distinctly improve the agreement between theory and experiment for very little extra work. The success of the corrected nucleation rate functions is surprising, given that they were developed based on experimental nucleation rates measured in a nucleation pulse chamber over a limited nucleation rate range 105<J/cm−3 s−1<1010, supersaturation range 6<S<22, and temperature range 220<T/K<260.

Barbara E. Wyslouzil

Papers

Invited review: secondary metabolism of hairy root cultures in bioreactors

Secondary metabolism of hairy root cultures in bioreactors

Freezing water in no-man's land

Binary nucleation in acid–water systems. II. Sulfuric acid–water and a comparison with methanesulfonic acid–water

Empirical function for homogeneous water nucleation rates