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

Polycyclic Hydrocarbons Vol. 1. Pp. xxvi + 487. 126S. (With a chapter on carcinogenesis by Regina Schoental.) Vol. 2. Pp. lvii + 487. 140s. By E. Clar. (London and New York: Academic Press; Berlin: Springer-Verlag, 1964.)

Polycyclic Aromatic Hydrocarbons

Chemical and microbial remediation of hexavalent chromium from contaminated soil and mining/metallurgical solid waste: a review.

Owing to their excellent multiplexing ability, high sensitivity, and large dynamic range, immunoassays using surface-enhanced Raman scattering (SERS) as the readout signal have found prosperous applications in fields such as disease diagnosis, environmental surveillance, and food safety supervision. Various ever-increasing demands have promoted SERS-based immunoassays from the classical sandwich-type ones to those integrated with fascinating automatic platforms (e.g., test strips and microfluidic chips). As recent years have witnessed impressive progress in SERS immunoassays, we try to comprehensively cover SERS-based immunoassays from their basic working principles to specific applications. Focusing on several basic elements in SERS immunoassays, typical structures of SERS nanoprobes, productive optical spectral encoding strategies, and popular immunoassay platforms are highlighted, followed by their representative biological applications in the last 5 years. Moreover, despite the vast advances achieved ...

SERS-Activated Platforms for Immunoassay: Probes, Encoding Methods, and Applications

https://repository.tudelft.nl/islandora/object/uuid%3Ab12d4d79-67af-4177-b03c-88bfaa8b622d/datastream/OBJ/download

A review on suppression and utilization of the coffee-ring effect.

In situ detection and identification of PAHs, a group of well-known persistent organic pollutants, presents a great challenge to environmental researchers. This work developed a novel substrate based on thiol-functionalized Fe3O4@Ag core–shell magnetic nanoparticles for surface enhanced Raman scattering (SERS) sensing of PAHs. The surface morphology, structure, and magnetic properties of the substrate were characterized using multiple complementary techniques including transmission electron microscopy, energy-dispersive X-ray spectroscopy, vibrating sample magnetometry analysis, and extended X-ray absorption fine structure spectroscopy. The high saturation magnetization at 48.35 emu g–1 enabled the complete and rapid separation of the substrate from the PAH solution. Benzene, naphthalene, anthracene, phenanthrene, fluorene, pyrene, perylene, and BaP were chosen as probe molecules. Qualitative and quantitative determination of PAHs was achieved using a portable Raman spectrometer. The SERS sensitivity was ...

Preparation of Thiol Modified Fe3O4@Ag Magnetic SERS Probe for PAHs Detection and Identification

Surface-enhanced Raman scattering (SERS) analysis of environmental hydrophobic pollutants without chemical functionalization of a bare nanoparticle (NP) substrate presents a challenge. The motivation for our study is to develop a highly reproducible and robust portable SERS sensor for detection and identification of polycyclic aromatic hydrocarbons (PAHs) using bare Au NPs. Our hypothesis is that the coffee ring effect could separate PAHs from the bulk solution and concentrate them on the closely packed Au NP ring, consequently enhancing their Raman scattering. This premise was confirmed with the commonly used citrate-reduced Au NPs in 20 nm, having no structural uniqueness. Because of the coffee ring effect, however, closely packed but not aggregated Au NP arrays were formed and, consequently, facilitated the separation and concentration of hydrophobic PAHs. As a result, a prominent SERS enhancement can be obtained on the ring because of the electromagnetic mechanism. A mixture of six PAHs with different numbers of benzene rings, namely, naphthalene, anthracene, pyrene, benzo[a]pyrene, benzo[g,h,i]perylene, and indeno[1,2,3-cd]pyrene, could be readily identified in river water. This portable SERS sensor based on the coffee ring effect provides a robust and versatile approach in PAH detection without the need for stringent structural requirements for Au NPs.

Facile detection of polycyclic aromatic hydrocarbons by a surface-enhanced Raman scattering sensor based on the Au coffee ring effect.

A novel sensitive and recyclable SERS substrate which can actively concentrate chromate (Cr(VI)) in water and substantially enhance Raman signal was synthesized as uniform Fe3O4@Ag nanoparticles. The surface morphology, structure, and magnetic properties were characterized using transmission electron microscopy, atomic force microscopy, X-ray powder diffraction, X-ray photoelectron spectroscopy, and vibrating sample magnetometry analysis. The closely spaced Fe3O4@Ag substrate with a core–shell structure exhibited a 25 nm surface roughness. The high saturation magnetization at 48.35 emu g−1 enabled the complete and rapid separation of the substrate from the solution. The sensitivity and reproducibility of the substrate were confirmed using a common SERS probe molecule, rhodamine 6G. SERS spectra of Cr(VI) in simulated and real contaminated water showed that the symmetric stretching vibrations of Cr–O occurred at 796 cm−1. This SERS peak area exhibited a linear dependence (R2 = 0.9992) on the Cr(VI) concentration between 5 and 100 μg L−1. Coexisting anions such as sulfate, nitrate, chloride, carbonate, and humic acid could decrease the sensitivity of the SERS analysis. However, the adverse effect of the competing ions may be eliminated by proper dilution of the raw sample. This study provides a reliable method for qualitative and quantitative analysis of Cr(VI).

Jingjing Du

Papers

Preparation of Thiol Modified Fe3O4@Ag Magnetic SERS Probe for PAHs Detection and Identification

Facile detection of polycyclic aromatic hydrocarbons by a surface-enhanced Raman scattering sensor based on the Au coffee ring effect.

Preparation of Fe3O4@Ag SERS substrate and its application in environmental Cr(VI) analysis.

Rapid in situ identification of arsenic species using a portable Fe3O4@Ag SERS sensor

Reduction and immobilization of chromate in chromite ore processing residue with nanoscale zero-valent iron