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

In several series of lithium, sodium, and potassium borosilicate glasses whose compositions traverse known regions of liquid–liquid phase separation, we have applied triple-quantum magic-angle spinning (3QMAS) 11B and 17O NMR to obtain high-resolution information about short-range structure and connections among various network structural units, and their variation with composition and thermal history. Oxygen-17 3QMAS spectra reveal changes in connectivities between silicate and BO3 ([3]B) and BO4 ([4]B) units, by quantifying populations of bridging oxygens such as B–O–B, Si–O–B and Si–O–Si, and of non-bridging oxygens. [3]B–O–Si and [4]B–O–Si as well as [3]B–O–[3]B and [4]B–O–[3]B linkages can be distinguished. 11B MAS and 3QMAS at a magnetic field of 14.1 T allow proportions of several borate units to be determined, including [3]B in boroxol ring and non-ring sites and [4]B with 3 versus 4 Si neighbors. By combining the 11B and 17O NMR results, detailed information on Si/B mixing in sodium borosilicates can be derived, showing, for example, that [4]B and non-ring [3]B tend to mix with silicate units, while ring [3]B is mainly connected to borate groups. In a preliminary study of the effects of varying alkali cation, potassium-containing glasses are similar to those in the sodium borosilicate system, but a lithium borosilicate seems to exhibit considerably greater chemical heterogeneity. In annealing experiments that converted an optically clear to obviously phase-separated glasses, the ratio of [3]B to [4]B does not change significantly, but part of the non-ring [3]B converts to ring [3]B as the degree of unmixing increases.

Solid-State NMR Study of Metastable Immiscibility in Alkali Borosilicate Glasses

All materials can suffer from environmental degradation; the rate and extent of degradation depend on the details of the material composition and structure as well as the environment. The corrosion of silicate glasses, crystalline ceramics, and metals, particularly as related to nuclear waste forms, has received a lot of attention. The corrosion phenomena and mechanisms of these materials are different, but also have many similarities. This review compares and contrasts the mechanisms of environmental degradation of glass, crystalline ceramics, and metals, with the goal of identifying commonalities that can seed synergistic activities and advance the current knowledge in each area.

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A comparative review of the aqueous corrosion of glasses, crystalline ceramics, and metals

Boron is considered to influence the performance of several metabolic enzymes and boron deficiency is associated with impaired growth and abnormal bone development. As such, boron is a beneficial bioactive element for animals and humans. It is also well known that boron stimulates wound healing and improves bone health. The addition of boron in different proportions to bioactive glasses has significant effects on glass structure, glass processing parameters, biodegradability, biocompatibility, bioactivity and cytotoxicity. Different compositions of bioactive glasses (BGs) containing boron, including boron-doped, borosilicate and borate glasses, are being investigated for bone and soft tissue engineering under the premise that these BGs are suitable carriers of boron, indicating controlled release of B species in the biological environment. This paper reviews up to date research and applications of borate, borosilicate, and boron doped silicate and phosphate BGs focussing on their physical, structural, degradation and biological properties for hard and soft tissue regeneration.

Boron-containing bioactive glasses in bone and soft tissue engineering

Development of boron oxide potentials for computer simulations of multicomponent oxide glasses

Knowing the structure of a material is necessary to understand its evolution under various influences; here, the alteration by water of a reference glass of nuclear interest, called International Simple Glass (ISG), is studied The ISG atomic structure has not yet been thoroughly characterized Short- and medium-range order in this six-oxide glass was investigated by molecular dynamics (MD) methods Combining the simulated data with experimental observations acquired from both pristine and altered ISG provided new insight into the formation of surface layers and passivation of the underlying glass In the tested conditions of 90 °C, silica-saturated solution, and pH90°C 7, the passivating layer partly inherits the structure of the pristine glass network despite the release of mobile elements (Na, B, and some Ca), with a reorganization of the silicate network following B release The layer appears to minimize its internal energy by relaxing strain accumulated during glass quenching The resulting passivated glass shows a strong resistance to hydrolysis The nanopores of this hydrated material, displaying a mean pore size of ∼1 nm, are filled with various water species Water speciation determination inside the nanopores is therefore an achievement for future water dynamic study in the passivated glass A combination of experiments and simulations has provided insight into the structural changes of a glass of nuclear interest in solution Borosilicate glasses are used as containment matrices for the highly radioactive waste that results from spent-nuclear-fuel reprocessing They are stored in deep geological repositories and while this is seen as a relatively long-term solution, how they respond to their environment is of obvious importance A team, led by Stephane Gin at the CEA, Marcoule, France, have now studied the changes that a reference glass known as International Simple Glass (ISG) undergoes when exposed to water Their simulations and analytical experiments provide insight into the structure of pristine ISG while also observing the generation of a passivating layer, which partly inherits the structure of the pristine glass but is less reactive with water

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Structure of International Simple Glass and properties of passivating layer formed in circumneutral pH conditions

A set of empirical potentials have been developed to enable molecular dynamics simulations of oxide glasses with the most common glass formers: silica, boron and aluminum oxides. Built upon the recent borosilicate potentials, this set of partial charge effective potentials features composition dependent variable atomic charges and pairwise short range interactions that ensure high computational efficiency. They can correctly reproduce the short range structure features of boroaluminosilicate glasses including [SiO4] tetrahedral network, aluminum coordination, and, importantly, the coordination change of boron as a function of composition. By using the newly developed potentials, a series of sodium boroaluminosilicate glasses were simulated and the structures analyzed in terms of bond distance, bond angle, and coordination number, which were compared with available theoretical, simulation and experimental results. Structural analysis such as polyhedral connectivity analysis, Qn analysis, and ring size distribution were obtained to investigate the medium range structure features of these glasses. Furthermore, mechanical properties such as Young's, shear and bulk moduli were calculated and were found to be in good agreement with experimental data. The vibrational density of states was also calculated and compared with previous MD and ab initio results. The results show [3]B and [4]B had distinctive spectra features and vibrational spectra were in good agreement with earlier ab initio studies.

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Development of effective empirical potentials for molecular dynamics simulations of the structures and properties of boroaluminosilicate glasses

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

We present the development of a ReaxFF reactive force field for Na/Si/O/H interactions, which enables reactive molecular dynamics simulation of the sodium silicate–water interfaces. The force field parameters were fitted against various quantum mechanical calculations, including equations of state of different NaSiOx crystalline phases, energy barriers of a sodium cation’s transport within the sodium silicate crystal structure, interactions between the hydroxylated silica surface and sodium cation–water systems, and dissociation energies of [NaOH–n(H2O)] (n = 1–6) clusters. After the optimization process, we validated the force field capability through calculating the structures of sodium silicate crystals and glasses and transport properties of sodium ions and protons within the amorphous structures. The force field was also applied to validate the dissociation behavior of sodium hydroxides within the bulk water. Our results with the developed force field are relevant to detailed chemical dissolution mec...

Lu Deng

Papers

Development of boron oxide potentials for computer simulations of multicomponent oxide glasses

Structure of International Simple Glass and properties of passivating layer formed in circumneutral pH conditions

Development of effective empirical potentials for molecular dynamics simulations of the structures and properties of boroaluminosilicate glasses

Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

Development of a ReaxFF Reactive Force Field for NaSiOx/Water Systems and Its Application to Sodium and Proton Self-Diffusion