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 antibacterial action of silver is utilized in numerous consumer products and medical devices. Metallic silver, silver salts, and also silver nanoparticles are used for this purpose. The state of research on the effect of silver on bacteria, cells, and higher organisms is summarized. It can be concluded that the therapeutic window for silver is narrower than often assumed. However, the risks for humans and the environment are probably limited.

Silver as Antibacterial Agent: Ion, Nanoparticle, and Metal

For nearly a decade, researchers have debated the mechanisms by which AgNPs exert toxicity to bacteria and other organisms. The most elusive question has been whether the AgNPs exert direct “particle-specific” effects beyond the known antimicrobial activity of released silver ions (Ag+). Here, we infer that Ag+ is the definitive molecular toxicant. We rule out direct particle-specific biological effects by showing the lack of toxicity of AgNPs when synthesized and tested under strictly anaerobic conditions that preclude Ag(0) oxidation and Ag+ release. Furthermore, we demonstrate that the toxicity of various AgNPs (PEG- or PVP- coated, of three different sizes each) accurately follows the dose–response pattern of E. coli exposed to Ag+ (added as AgNO3). Surprisingly, E. coli survival was stimulated by relatively low (sublethal) concentration of all tested AgNPs and AgNO3 (at 3–8 μg/L Ag+, or 12–31% of the minimum lethal concentration (MLC)), suggesting a hormetic response that would be counterproductive t...

Negligible Particle-Specific Antibacterial Activity of Silver Nanoparticles

Recent advances in nanoscience and nanotechnology radically changed the way we diagnose, treat, and prevent various diseases in all aspects of human life. Silver nanoparticles (AgNPs) are one of the most vital and fascinating nanomaterials among several metallic nanoparticles that are involved in biomedical applications. AgNPs play an important role in nanoscience and nanotechnology, particularly in nanomedicine. Although several noble metals have been used for various purposes, AgNPs have been focused on potential applications in cancer diagnosis and therapy. In this review, we discuss the synthesis of AgNPs using physical, chemical, and biological methods. We also discuss the properties of AgNPs and methods for their characterization. More importantly, we extensively discuss the multifunctional bio-applications of AgNPs; for example, as antibacterial, antifungal, antiviral, anti-inflammatory, anti-angiogenic, and anti-cancer agents, and the mechanism of the anti-cancer activity of AgNPs. In addition, we discuss therapeutic approaches and challenges for cancer therapy using AgNPs. Finally, we conclude by discussing the future perspective of AgNPs.

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Silver Nanoparticles: Synthesis, Characterization, Properties, Applications, and Therapeutic Approaches

Silver nanoparticles (Ag-NPs) readily transform in the environment, which modifies their properties and alters their transport, fate, and toxicity. It is essential to consider such transformations when assessing the potential environmental impact of Ag-NPs. This review discusses the major transformation processes of Ag-NPs in various aqueous environments, particularly transformations of the metallic Ag cores caused by reactions with (in)organic ligands, and the effects of such transformations on physical and chemical stability and toxicity. Thermodynamic arguments are used to predict what forms of oxidized silver will predominate in various environmental scenarios. Silver binds strongly to sulfur (both organic and inorganic) in natural systems (fresh and sea waters) as well as in wastewater treatment plants, where most Ag-NPs are expected to be concentrated and then released. Sulfidation of Ag-NPs results in a significant decrease in their toxicity due to the lower solubility of silver sulfide, potentiall...

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Environmental transformations of silver nanoparticles: impact on stability and toxicity.

Many important aspects of nanosilver behavior are influenced by the ionic activity associated with the particle suspension, including antibacterial potency, eukaryotic toxicity, environmental release, and particle persistence. The present study synthesizes pure, ion-free, citrate-stabilized nanosilver (nAg) colloids as model systems, and measures their time-dependent release of dissolved silver using centrifugal ultrafiltration and atomic absorption spectroscopy. Ion release is shown to be a cooperative oxidation process requiring both dissolved dioxygen and protons. It produces peroxide intermediates, and proceeds to complete reactive dissolution under some conditions. Ion release rates increase with temperature in the range 0−37 °C, and decrease with increasing pH or addition of humic or fulvic acids. Sea salts have only a minor effect on dissolved silver release. Silver nanoparticle surfaces can adsorb Ag+, so even simple colloids contain three forms of silver: Ag0 solids, free Ag+ or its complexes, an...

Ion Release Kinetics and Particle Persistence in Aqueous Nano-Silver Colloids

Major pathways in the antibacterial activity and eukaryotic toxicity of nanosilver involve the silver cation and its soluble complexes, which are well established thiol toxicants. Through these pathways, nanosilver behaves in analogy to a drug delivery system, in which the particle contains a concentrated inventory of an active species, the ion, which is transported to and released near biological target sites. Although the importance of silver ion in the biological response to nanosilver is widely recognized, the drug delivery paradigm has not been well developed for this system, and there is significant potential to improve nanosilver technologies through controlled release formulations. This article applies elements of the drug delivery paradigm to nanosilver dissolution and presents a systematic study of chemical concepts for controlled release. After presenting thermodynamic calculations of silver species partitioning in biological media, the rates of oxidative silver dissolution are measured for nan...

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Controlled release of biologically active silver from nanosilver surfaces

The widespread use of silver nanoparticles (Ag-NPs) in consumer and medical products provides strong motivation for a careful assessment of their environmental and human health risks. Recent studies have shown that Ag-NPs released to the natural environment undergo profound chemical transformations that can affect silver bioavailability, toxicity, and risk. Less is known about Ag-NP chemical transformations in biological systems, though the medical literature clearly reports that chronic silver ingestion produces argyrial deposits consisting of silver-, sulfur-, and selenium-containing particulate phases. Here we show that Ag-NPs undergo a rich set of biochemical transformations, including accelerated oxidative dissolution in gastric acid, thiol binding and exchange, photoreduction of thiol- or protein-bound silver to secondary zerovalent Ag-NPs, and rapid reactions between silver surfaces and reduced selenium species. Selenide is also observed to rapidly exchange with sulfide in preformed Ag2S solid phas...

http://www.nseresearch.org/2012/posters/Jingyu_Liu_Zhongying_Want_Agnes_Kane_Robert_Hurt~Hurt_poster.pdf

Chemical transformations of nanosilver in biological environments.

Among the many new engineered nanomaterials, nanosilver is one of the highest priority cases for environmental risk assessment. Recent analysis of field samples from water treatment facilities suggests that silver is converted to silver sulfide, whose very low solubility may limit the bioavailability and adverse impact of silver in the environment. The present study demonstrates that silver nanoparticles react with dissolved sulfide species (H(2)S, HS(-)) under relevant but controlled laboratory conditions to produce silver sulfide nanostructures similar to those observed in the field. The reaction is tracked by time-resolved sulfide depletion measurements to yield quantitative reaction rates and stoichiometries. The reaction requires dissolved oxygen, and it is sensitive to pH and natural organic matter. Focused-ion-beam analysis of surface films reveals an irregular coarse-grained sulfide phase that allows deep (>1 μm) conversion of silver surfaces without passivation. At high sulfide concentrations, nanosilver oxysulfidation occurs by a direct particle-fluid reaction. At low sulfide concentration, quantitative kinetic analysis suggests a mechanistic switch to an oxidative dissolution/precipitation mechanism, in which the biologically active Ag(+) ion is generated as an intermediate. The environmental transformation pathways for nanosilver will vary depending on the media-specific competing rates of oxidative dissolution and direct oxysulfidation.

Kinetics and mechanisms of nanosilver oxysulfidation.

Water microdroplets containing graphene oxide and a second solute are shown to spontaneously segregate into sack-cargo nanostructures upon drying. Analytical modeling and molecular dynamics suggest the sacks form when slow-diffusing graphene oxide preferentially accumulates and adsorbs at the receding air–water interface, followed by capillary collapse. Cargo-filled graphene nanosacks can be nanomanufactured by a simple, continuous, scalable process and are promising for many applications where nanoscale materials should be isolated from the environment or biological tissue.

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Jingyu Liu

Papers

Ion Release Kinetics and Particle Persistence in Aqueous Nano-Silver Colloids

Controlled release of biologically active silver from nanosilver surfaces

Chemical transformations of nanosilver in biological environments.

Kinetics and mechanisms of nanosilver oxysulfidation.

Aerosol synthesis of cargo-filled graphene nanosacks.