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

Since the discovery of mechanically exfoliated graphene in 2004, research on ultrathin two-dimensional (2D) nanomaterials has grown exponentially in the fields of condensed matter physics, material science, chemistry, and nanotechnology. Highlighting their compelling physical, chemical, electronic, and optical properties, as well as their various potential applications, in this Review, we summarize the state-of-art progress on the ultrathin 2D nanomaterials with a particular emphasis on their recent advances. First, we introduce the unique advances on ultrathin 2D nanomaterials, followed by the description of their composition and crystal structures. The assortments of their synthetic methods are then summarized, including insights on their advantages and limitations, alongside some recommendations on suitable characterization techniques. We also discuss in detail the utilization of these ultrathin 2D nanomaterials for wide ranges of potential applications among the electronics/optoelectronics, electrocat...

Recent Advances in Ultrathin Two-Dimensional Nanomaterials

Metal species with different size (single atoms, nanoclusters, and nanoparticles) show different catalytic behavior for various heterogeneous catalytic reactions. It has been shown in the literature that many factors including the particle size, shape, chemical composition, metal–support interaction, and metal–reactant/solvent interaction can have significant influences on the catalytic properties of metal catalysts. The recent developments of well-controlled synthesis methodologies and advanced characterization tools allow one to correlate the relationships at the molecular level. In this Review, the electronic and geometric structures of single atoms, nanoclusters, and nanoparticles will be discussed. Furthermore, we will summarize the catalytic applications of single atoms, nanoclusters, and nanoparticles for different types of reactions, including CO oxidation, selective oxidation, selective hydrogenation, organic reactions, electrocatalytic, and photocatalytic reactions. We will compare the results o...

Metal Catalysts for Heterogeneous Catalysis: From Single Atoms to Nanoclusters and Nanoparticles.

Single-atom catalysis has arguably become the most active new frontier in heterogeneous catalysis. Aided by recent advances in practical synthetic methodologies, characterization techniques and computational modelling, we now have a large number of single-atom catalysts (SACs) that exhibit distinctive performances for a wide variety of chemical reactions. This Perspective summarizes recent experimental and computational efforts aimed at understanding the bonding in SACs and how this relates to catalytic performance. The examples described here illustrate the utility of SACs in a broad scope of industrially important reactions and highlight the advantages these catalysts have over those presently used. SACs have well-defined active centres, such that unique opportunities exist for the rational design of new catalysts with high activities, selectivities and stabilities. Indeed, given a certain practical application, we can often design a suitable SAC; thus, the field has developed very rapidly and afforded promising catalyst leads. Moreover, the control we have over certain SAC structures paves the way for designing base metal catalysts with the activities of noble metal catalysts. It appears that we are entering a new era of heterogeneous catalysis in which we have control over well-dispersed single-atom active sites whose properties we can readily tune. Single-atom catalysts are heterogeneous materials featuring active metals sites atomically dispersed on a surface. This Review describes methods by which we prepare and characterize these materials, as well as how we can tune their catalytic performance in a variety of important reactions.

Heterogeneous single-atom catalysis

A new strategy for achieving stable Co single atoms (SAs) on nitrogen-doped porous carbon with high metal loading over 4 wt % is reported. The strategy is based on a pyrolysis process of predesigned bimetallic Zn/Co metal–organic frameworks, during which Co can be reduced by carbonization of the organic linker and Zn is selectively evaporated away at high temperatures above 800 °C. The spherical aberration correction electron microscopy and extended X-ray absorption fine structure measurements both confirm the atomic dispersion of Co atoms stabilized by as-generated N-doped porous carbon. Surprisingly, the obtained Co-Nx single sites exhibit superior ORR performance with a half-wave potential (0.881 V) that is more positive than commercial Pt/C (0.811 V) and most reported non-precious metal catalysts. Durability tests revealed that the Co single atoms exhibit outstanding chemical stability during electrocatalysis and thermal stability that resists sintering at 900 °C. Our findings open up a new routine for general and practical synthesis of a variety of materials bearing single atoms, which could facilitate new discoveries at the atomic scale in condensed materials.

Single Cobalt Atoms with Precise N-Coordination as Superior Oxygen Reduction Reaction Catalysts

Temperature plays a critical role in regulating body mechanisms and indicating inflammatory processes. Local temperature increments above 42°C have been shown to kill cancer cells in tumorous tissue, leading to the development of nanoparticle-mediated thermo-therapeutic strategies for fighting oncological diseases. Remarkably, these therapeutic effects can occur without macroscopic temperature rise, suggesting localized nanoparticle heating, minimizing side effects on healthy tissues. Nanothermometry has received considerable attention as a means of developing nanothermosensing approaches to monitor the temperature at the core of nanoparticle atoms inside cells. In this study, a label-free, direct, and universal nanoscale thermometry was proposed to monitor the thermal processes of nanoparticles under photoexcitation in the tumour environment. Gold-iron oxide nanohybrids were utilized as multifunctional photothermal agents internalized in a 3D tumour model of glioblastoma that mimics the in vivo scenario. The local temperature under near-infrared photo-excitation was monitored by X-ray absorption spectroscopy at the Au L3 -edge (11900 eV) to obtain their temperature in cells, deepening our knowledge of nanothermal tumour treatments. This nanothermometric approach demonstrates its potential in detecting high nanothermal changes in tumor-mimicking tissues. It offers a notable advantage by enabling thermal sensing of any element, effectively transforming any material into a nanothermometer within biological environments. This article is protected by copyright. All rights reserved.

X-ray Nanothermometry of Nanoparticles in Tumour-Mimicking Tissues Under Photothermia.

We have studied the amorphization process of SnI4 up to 26.8GPa with unprecedented experimental details by combining Sn and I K edge X-ray absorption spectroscopy and powder X-ray diffraction. Standards and reverse Monte Carlo extended X-ray absorption fine structure (EXAFS) refinements confirm that the SnI4 tetrahedron is a fundamental structural unit that is preserved through the crystalline phase-I to crystalline phase-II transition about 7 to 10GPa and then in the amorphous phase that appears above 20GPa. Up to now unexploited Iodine EXAFS reveals to be extremely informative and confirms the formation of iodine iodine short bonds close to 2.85A in the amorphous phase at 26.8 GPa. A coordination number increase of Sn in the crystalline phase-II appears to be excluded, while the deformation of the tetrahedral units proceeds through a flattening that keeps the average I-Sn-I angle close to 109.5°. Moreover, we put in evidence the impact of pressure on the Sn near edge structure under competing geometrical and electronic effects.

Mechanism of pressure induced amorphization of SnI4: a combined X-ray diffraction -- X-ray absorption spectroscopy study

One of the main challenges in Environmental sciences is the identification and chemical evolution of polluting traces (e.g, cadmium or antimony) in soil, which requires long acquistion times for accurate measurements at synchrotron facilities. In this context, the potential of a new generation multi-element germanium detectors to identify traces at 0.1-1 ppm in a reasonable time has been studied using Allpix Squared framework [1]. This code has been customized to include the three dimensional electric and weighting field maps generated by COMSOL Multiphysics software, and several features to model the sample environment at SOLEIL synchrotron and the signal response of a germanium detector equipped with a Digital Pulse Processor (DPP). The full simulation chain has been validated by experimental data from SAMBA beamline of SOLEIL synchrotron. This work presents a first estimation of the detection limit to cadmium traces in a soil sample for a future multi-element germanium detector, using this simulation chain.

https://doi.org/10.1088/1742-6596/2380/1/012096

Emiliano Fonda

Papers

X-ray Nanothermometry of Nanoparticles in Tumour-Mimicking Tissues Under Photothermia.

Mechanism of pressure induced amorphization of SnI4: a combined X-ray diffraction -- X-ray absorption spectroscopy study

Detection limit of next-generation of multi-element germanium detectors in the context of Environmental science