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 science and technology of ultracapacitors are reviewed for a number of electrode materials, including carbon, mixed metal oxides, and conducting polymers. More work has been done using microporous carbons than with the other materials and most of the commercially available devices use carbon electrodes and an organic electrolytes. The energy density of these devices is 3¯5 Wh/kg with a power density of 300¯500 W/kg for high efficiency (90¯95%) charge/discharges. Projections of future developments using carbon indicate that energy densities of 10 Wh/kg or higher are likely with power densities of 1¯2 kW/kg. A key problem in the fabrication of these advanced devices is the bonding of the thin electrodes to a current collector such the contact resistance is less than 0.1 cm2. Special attention is given in the paper to comparing the power density characteristics of ultracapacitors and batteries. The comparisons should be made at the same charge/discharge efficiency.

Ultracapacitors: Why, How, and Where is the Technology

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Over the past few decades, the design and development of advanced electrocatalysts for efficient energy conversion technologies have been subjects of extensive study. With the discovery of graphene, two-dimensional (2D) nanomaterials have emerged as some of the most promising candidates for heterogeneous electrocatalysts due to their unique physical, chemical, and electronic properties. Here, we review 2D-nanomaterial-based electrocatalysts for selected electrocatalytic processes. We first discuss the unique advances in 2D electrocatalysts based on different compositions and functions followed by specific design principles. Following this overview, we discuss various 2D electrocatalysts for electrocatalytic processes involved in the water cycle, carbon cycle, and nitrogen cycle from their fundamental conception to their functional application. We place a significant emphasis on different engineering strategies for 2D nanomaterials and the influence these strategies have on intrinsic material performance, ...

Emerging Two-Dimensional Nanomaterials for Electrocatalysis

Reactive oxygen species (ROS) play an essential role in regulating various physiological functions of living organisms. The intrinsic biochemical properties of ROS, which underlie the mechanisms ne...

Reactive Oxygen Species (ROS)-Based Nanomedicine.

Phosphorus is a nonmetal with several allotropes, from the highly reactive white phosphorus to the thermodynamically stable black phosphorus (BP) with a puckered orthorhombic layered structure. The bulk form of BP was first synthesized in 1914, but received little attention until it was rediscovered in 2014 as a member of the new wave of 2D layered nanomaterials. BP can be exfoliated to a single sheet that acts as a semiconductor with a tunable direct band gap, a high carrier mobility at room temperature, and an in-plane anisotropy. The development of BP applications is hampered by surface degradation, thus efforts to achieve effective BP passivation are ongoing, such as its integration in van der Waals heterostructures. BP has been tested as a novel nanomaterial in batteries, transistors, sensors, and photonics. This Review begins with the origin of the BP story, following the path from a bulk material to modern few/single layers. The physical and chemical properties are summarized, and the state-of-the-art of BP applications highlighted.

Black Phosphorus Rediscovered: From Bulk Material to Monolayers

The demand for simple, sensitive, affordable, and selective DNA biosensors is ubiquitous, due to the important role that DNA detection performs in the areas of disease diagnostics, environment monitoring, and food safety. A novel application of carboxylic carbon quantum dots (cCQD) is highlighted in this study. Herein, cCQD function as a nanoquencher in the detection of nucleic acid based on a homogeneous fluorescent assay. To that purpose, the performance of two types of cCQD, namely, citric acid QD and malic acid QD, is evaluated. The principle behind the sensing of nucleic acid lies in the different propensity of single-stranded DNA and double-stranded DNA to adsorb onto the surface of cCQD. For both types of cCQD, a superior range of detection of at least 3 orders of magnitude is achieved, and the potential to distinguish single-base mismatch is also exhibited. These findings are anticipated to provide valuable insights on the employment of cCQD for the fabrication of future DNA biosensors.

Carboxylic Carbon Quantum Dots as a Fluorescent Sensing Platform for DNA Detection

Layered transition metal dichalcogenides (TMDs) have been the center of attention in the scientific community due to their properties that can be tapped on for applications in electrochemistry and hydrogen evolution reaction (HER) catalysis. We report on the effect of electrochemical treatment of exfoliated MoS2, WS2, MoSe2 and WSe2 nanosheets toward the goal of activating the electrochemical and HER catalytic properties of the TMDs. In particular, electrochemical activation of the heterogeneous electron transfer (HET) abilities of MoS2, MoSe2 and WSe2 is achieved via reductive treatments at identified reductive potentials based on their respective inherent electrochemistry. Comparing all TMDs, the charge transfer activation is most accentuated in MoSe2 and can be concluded that Mo metal and Se chalcogen type are more susceptible to electrochemical activation than W metal and S chalcogen type. With regards to the HER, we show that while MoS2 displayed enhanced performance when subjected to electrochemical...

Catalytic and Charge Transfer Properties of Transition Metal Dichalcogenides Arising from Electrochemical Pretreatment

Black phosphorus (BP), the latest addition to the family of 2D layered materials, has attracted much interest owing to potential optoelectronics, nanoelectronics, and biomedicine applications. Little is known about its toxicity, such as whether it could be as toxic as white phosphorus. In response to the possibility of BP employment into commercial products and biomedical devices, its cytotoxicity to human lung carcinoma epithelial cells (A549) was investigated. Following a 24 h exposure of the cells with different BP concentrations, cell viability assessments were conducted using water-soluble tetrazolium salt (WST-8) and methylthiazolyldiphenyltetrazolium bromide (MTT) assays. The toxicological effects were found to be dose-dependent, with BP reducing cell viabilities to 48% (WST-8) and 34% (MTT) at 50 μg mL(-1) exposure. This toxicity was observed to be generally intermediate between that of graphene oxides and exfoliated transition-metal dichalcogenides (MoS2, WS2, WSe2). The relatively low toxicity paves the way to utilization of black phosphorus.

Zdenek Sofer

Papers

Black Phosphorus Rediscovered: From Bulk Material to Monolayers

Carboxylic Carbon Quantum Dots as a Fluorescent Sensing Platform for DNA Detection

Catalytic and Charge Transfer Properties of Transition Metal Dichalcogenides Arising from Electrochemical Pretreatment

The Cytotoxicity of Layered Black Phosphorus

Will Any Crap We Put into Graphene Increase Its Electrocatalytic Effect