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

A systematic and detailed study for size-specific antibacterial efficacy of silver nanoparticles (AgNPs) synthesized using a co-reduction approach is presented here. Nucleation and growth kinetics during the synthesis process was precisely controlled and AgNPs of average size 5, 7, 10, 15, 20, 30, 50, 63, 85, and 100 nm were synthesized with good yield and monodispersity. We found the bacteriostatic/bactericidal effect of AgNPs to be size and dose-dependent as determined by the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of silver nanoparticles against four bacterial strains. Out of the tested strains, Escherichia coli MTCC 443 and Staphylococcus aureus NCIM 5201 were found to be the most and least sensitive strains regardless of AgNP size. For AgNPs with less than 10 nm size, the antibacterial efficacy was significantly enhanced as revealed through delayed bacterial growth kinetics, corresponding MIC/MBC values and disk diffusion tests. AgNPs of the smallest size, i.e., 5 nm demonstrated the best results and mediated the fastest bactericidal activity against all the tested strains compared to AgNPs having 7 nm and 10 nm sizes at similar bacterial concentrations. TEM analysis of AgNP treated bacterial cells showed the presence of AgNPs on the cell membrane, and AgNPs internalized within the cells.

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Size-controlled silver nanoparticles synthesized over the range 5–100 nm using the same protocol and their antibacterial efficacy

The nucleation of crystals in liquids is one of nature’s most ubiquitous phenomena, playing an important role in areas such as climate change and the production of drugs. As the early stages of nucleation involve exceedingly small time and length scales, atomistic computer simulations can provide unique insights into the microscopic aspects of crystallization. In this review, we take stock of the numerous molecular dynamics simulations that, in the past few decades, have unraveled crucial aspects of crystal nucleation in liquids. We put into context the theoretical framework of classical nucleation theory and the state-of-the-art computational methods by reviewing simulations of such processes as ice nucleation and the crystallization of molecules in solutions. We shall see that molecular dynamics simulations have provided key insights into diverse nucleation scenarios, ranging from colloidal particles to natural gas hydrates, and that, as a result, the general applicability of classical nucleation theory...

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

The aggregative growth and oriented attachment of nanocrystals and nanoparticles are reviewed, and they are contrasted to classical LaMer nucleation and growth, and to Ostwald ripening. Kinetic and mechanistic models are presented, and experiments directly observing aggregative growth and oriented attachment are summarized. Aggregative growth is described as a nonclassical nucleation and growth process. The concept of a nucleation function is introduced, and approximated with a Gaussian form. The height (Γmax) and width (Δtn) of the nucleation function are systematically varied by conditions that influence the colloidal stability of the small, primary nanocrystals participating in aggregative growth. The nucleation parameters Γmax and Δtn correlate with the final nanocrystal mean size and size distribution, affording a potential means of achieving nucleation control in nanocrystal synthesis.

Kinetics and Mechanisms of Aggregative Nanocrystal Growth

A theory is developed which allows one to discuss the stability of multiply-twinned particles and to calculate critical sizes for stable and quasi-stable states. An icosahedral particle is essentially stable for r ≦ r i w * , quasi-stable for r i w * r i t 0 where r is an edge length of the particle, while a decahedral particle is not essentially stable but quasi-stable for r ≦ r d t 0 and unstable for r > r d t 0 . The critical sizes r i w * , r i t 0 and r d t 0 are formulated as functions of the specific surface energy γ h k l , the twin boundary energy γ t , the elastic strain energy W and the adhesive energy γ a to the substrate. Calculated critical diameters 2 r i w * ,2 r i t 0 and 2 r d t 0 for the particles grown in free space for several elements range between 15.5A and 106.8A, between 109.8A and 486.1A and between 725A and 3961A, respectively. These values are in good agreement with experimental results.

Stability of Multiply-Twinned Particles

We present a novel method to identify local structures in disordered systems according to topological criteria. Its effectiveness is demonstrated in the analysis of the atomic structures in the rapid cooling of silver liquid. The method is parameter free and scale independent, and can generally be used for structural analysis of amorphous systems involving atoms or particles at different length scales.

https://iopscience.iop.org/article/10.1209/0295-5075/96/36001/pdf

A new method for analyzing the local structures of disordered systems

A molecular dynamics simulation study has been performed to investigate the solid microstructures of Ag at room temperature resulted from rapid solidification with six cooling rates by using Quantum Sutton–Chen (QSC) many body potential. Several structural analysis methods have been employed to characterize and analyze the atomic configurations in the system. The results reveal that as the cooling rate γ ⩾ 1.0 × 10 13  K/s, an amorphous structure can be obtained; as the cooling rates in the range of γ = 5.0 × 10 12  ∼ 1.38 × 10 11  K/s, the coexistence structures of the meta-stable hcp with stable fcc configurations can be formed with phase separating or layering structures. Moreover, by using the 3D graphics technology, the arrangement of atoms in the system reveals that the phase separating occurs before the layering structures can be formed following the cooling rate decreasing. And an interesting layering structures have been found, in which the central atoms of fcc and hcp basic clusters are arranged by alternate close-packed-layers with a new repeating sequence ABCB.

Molecular dynamics simulation for cooling rate dependence of solidification microstructures of silver

The effect of the cooling rate on the solidification process of liquid aluminium is studied using a large-scale molecular dynamics method. It is found that there are various types of short-range order (SRO) structures in the liquid, among which the icosahedral (ICO)-like structures are dominant. These SRO structures are in dynamic fluctuation and transform each other. The effect of the cooling rate on the microstructure is very weak at high temperatures and in supercooled liquids, and it appears only below the liquid–solid transition temperature. Fast cooling rates favour the formation of amorphous structures with ICO-like features, while slow cooling rates favour the formation of FCC crystalline structures. Furthermore, FCC and HCP structures can coexist in crystalline structures. It is also found that nanocrystalline aluminium can be achieved at appropriate cooling rates, and its formation mechanism is thoroughly investigated by tracing the evolution of nanoclusters. The arrangement of FCC and HCP atoms in the nanograins displays various twinned structures as observed using visualization analysis, which is different from the layering or phase separation structures observed in the solidification of Lennard-Jones fluids and some metal liquids.

Cooling rate dependence of solidification for liquid aluminium: a large-scale molecular dynamics simulation study

Some glass-forming liquids have different liquid phases that have the same composition but different structure, density and entropy Based on experimental and molecular dynamics simulation, we here report thermodynamic, dynamic, and structural evidence of the liquid–liquid transition (LLT) in ten Cu–Zr glass-forming liquids well above the liquidus temperature We find that for Cu–Zr alloys, the LLT is beneficial to glass formation, and there is a close relationship between the relative transition strength (RTS) of the LLT and the critical thickness representing the glass forming ability (GFA): the bigger the value of the RTS parameters, the stronger the GFA of Cu–Zr alloys This work not only uncovers the role of the LLT of melts in the glass formation of solids, but also sheds light on the inheritance of properties of glassy solids from the aspect of the detectable dynamics of high-temperature melts

The role of liquid-liquid transition in glass formation of CuZr alloys

The structural evolution of tantalum (Ta) during rapid cooling was investigated by molecular dynamics simulation, in terms of the system energy, the pair distribution function and the largest standard cluster analysis. It was found that the critical cooling rate for vitrification was about R ≥ 0.25 K ps−1, two orders lower than other metals (such as Au, Ag, Al, Zr and Zn) and that the meta-stable σ phase (β-Ta) not only appears on the pathway from liquid to the stable body-centred cubic crystal, but is also easily obtained at room temperature as a long-lived metastable phase with some probability. The most interesting point is that the liquid, amorphous and β-Ta phases share a nontrivial structural homology; the intrinsic topologically close-packed (TCP) structures in liquids are inherited and developed in different ways, resulting in amorphous or crystalline solids, respectively. With highly local packing fractions and geometrical incompatibility with the global close-packed (such as hcp, fcc and bcc) crystals, TCP structures inevitably result in structural heterogeneity and favour vitrification. As a superset of icosahedrons, TCP structures are ubiquitous in metallic melts, and just before the onset of crystallization reach their maximal number, which is much bigger in Ta than in other poor-GFA metals; so we argue that the strong forming ability of TCP local structures significantly enhances the glass forming ability of pure metals. These findings open up a new perspective that could have a profound impact on the research into metallic glasses.

Zean Tian

Papers

A new method for analyzing the local structures of disordered systems

Molecular dynamics simulation for cooling rate dependence of solidification microstructures of silver

Cooling rate dependence of solidification for liquid aluminium: a large-scale molecular dynamics simulation study

The role of liquid-liquid transition in glass formation of CuZr alloys

Topologically close-packed characteristic of amorphous tantalum.