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

For decades, studies of endocrine-disrupting chemicals (EDCs) have challenged traditional concepts in toxicology, in particular the dogma of “the dose makes the poison,” because EDCs can have effects at low doses that are not predicted by effects at higher doses. Here, we review two major concepts in EDC studies: low dose and nonmonotonicity. Low-dose effects were defined by the National Toxicology Program as those that occur in the range of human exposures or effects observed at doses below those used for traditional toxicological studies. We review the mechanistic data for low-dose effects and use a weight-of-evidence approach to analyze five examples from the EDC literature. Additionally, we explore nonmonotonic dose-response curves, defined as a nonlinear relationship between dose and effect where the slope of the curve changes sign somewhere within the range of doses examined. We provide a detailed discussion of the mechanisms responsible for generating these phenomena, plus hundreds of examples from...

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Hormones and endocrine-disrupting chemicals: Low-dose effects and nonmonotonic dose responses

The science of the total environment

Plastics debris in the marine environment, including resin pellets, fragments and microscopic plastic fragments, contain organic contaminants, including polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons, petroleum hydrocarbons, organochlorine pesticides (2,2′-bis(p-chlorophenyl)-1,1,1-trichloroethane, hexachlorinated hexanes), polybrominated diphenylethers, alkylphenols and bisphenol A, at concentrations from sub ng g–1 to µg g–1. Some of these compounds are added during plastics manufacture, while others adsorb from the surrounding seawater. Concentrations of hydrophobic contaminants adsorbed on plastics showed distinct spatial variations reflecting global pollution patterns. Model calculations and experimental observations consistently show that polyethylene accumulates more organic contaminants than other plastics such as polypropylene and polyvinyl chloride. Both a mathematical model using equilibrium partitioning and experimental data have demonstrated the transfer of contaminants from plastic to organisms. A feeding experiment indicated that PCBs could transfer from contaminated plastics to streaked shearwater chicks. Plasticizers, other plastics additives and constitutional monomers also present potential threats in terrestrial environments because they can leach from waste disposal sites into groundwater and/or surface waters. Leaching and degradation of plasticizers and polymers are complex phenomena dependent on environmental conditions in the landfill and the chemical properties of each additive. Bisphenol A concentrations in leachates from municipal waste disposal sites in tropical Asia ranged from sub µg l–1 to mg l–1 and were correlated with the level of economic development.

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Transport and release of chemicals from plastics to the environment and to wildlife

Initial-value ordinary differential equation solution via variable order Adams method (SIVA/DIVA) package is collection of subroutines for solution of nonstiff ordinary differential equations. There are versions for single-precision and double-precision arithmetic. Requires fewer evaluations of derivatives than other variable-order Adams predictor/ corrector methods. Option for direct integration of second-order equations makes integration of trajectory problems significantly more efficient. Written in FORTRAN 77.

Solving Ordinary Differential Equations

General aspects chemical aspects analytical aspects geobotanical and biogeochemical prospecting and analysis for heavy metal deposits biomonitoring terrestrial heavy metal pollution by plants - lichens, fungi, mosses, higher plants analysis of heavy metals in plants for the selection of future monitoring species.

Plants as biomonitors : indicators for heavy metals in the terrestrial environment

The effects of suspected endocrine disrupting chemicals on freshwater and marine prosobranch species were analysed in laboratory experiments In this first publication, the responses of the freshwater snail Marisa cornuarietis and of the marine prosobranch Nucella lapillus to the xeno-estrogenic model compounds bisphenol A (BPA) and octylphenol (OP) are presented at nominal concentration ranges between 1 and 100 micrograms/L Marisa was exposed during 5 months using adult specimens and in a complete life-cycle test for 12 months In both experiments, the xeno-estrogens induced a complex syndrome of alterations in female Marisa referred to as "superfemales" at the lowest concentrations Affected specimens were characterised by the formation of additional female organs, an enlargement of the accessory pallial sex glands, gross malformations of the pallial oviduct section resulting in an increased female mortality, and a massive stimulation of oocyte and spawning mass production The effects of BPA and OP were comparable at the same nominal concentrations An exposure to OP resulted in inverted U-type concentration response relationships for egg and spawning mass production Adult Nucella from the field were tested for three months in the laboratory As in Marisa, superfemales with enlarged accessory pallial sex glands and an enhancement of oocyte production were observed No oviduct malformations were found probably due to species differences in the gross anatomical structure of the pallial oviduct A lower percentage of exposed specimens had ripe sperm stored in their vesicula seminalis and additionally male Nucella exhibited a reduced length of penis and prostate gland when compared to the control Because statistically significant effects were observed at the lowest nominal test concentrations (1 microgram BPA or OP/L), it can be assumed that even lower concentrations may have a negative impact on the snails The results show that prosobranchs are sensitive to endocrine disruption at environmentally relevant concentrations and that especially M cornuarietis is a promising candidate for a future organismic invertebrate model to identify endocrine-mimetic test compounds

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Effects of endocrine disruptors on prosobranch snails (Mollusca: Gastropoda) in the laboratory. Part I: Bisphenol A and octylphenol as xeno-estrogens.

A systematic review of gait analysis methods based on inertial sensors and adaptive algorithms.

Bioindicators and biomonitors: principles, concepts and applications.

In the context of environmental monitoring studies bioindicators reflect organisms (or parts of organisms or communities of organisms) that contain information on quality of the environment (or a part of the environment). Biomonitors, on the other hand, are organisms (or parts of organisms or communities of organisms) that contain informations on the quantitative aspects of quality of the environment. When data and information obtained by bioindication are moved up to the level of knowledge the subjectivity of interpretation increases with the complexity and dynamics of a system (“staircase of knowing”). In this article clearcut definitions are attempted for most terms used in environmental monitoring studies. From there a comparison of instrumental measurements with the use of bioindicators/biomonitors with respect to harmonisation and quality control will be drawn. Precision, accuracy, calibration and harmonisation in between national standards and international routines seem to be the leading goals in quality studies of international working groups dealing with biomonitoring throughout the world. Common strategies and concepts will fill the gap in between single source results and integrated approaches related either for human health aspects or environmental protection purposes, f.e. via biodiversity monitoring. Here we report on well established monitoring programmes like Environmental Specimen Banking (ESB) or newly developed strategies as the Multi-Markered Bioindication Concept (MMBC) with its functional and integrated windows of prophylactic health care.

Bernd Markert

Papers

Plants as biomonitors : indicators for heavy metals in the terrestrial environment

Effects of endocrine disruptors on prosobranch snails (Mollusca: Gastropoda) in the laboratory. Part I: Bisphenol A and octylphenol as xeno-estrogens.

A systematic review of gait analysis methods based on inertial sensors and adaptive algorithms.

Bioindicators and biomonitors: principles, concepts and applications.

Chapter 1 Definitions, strategies and principles for bioindication/biomonitoring of the environment