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

Quantum metrology enables some of the most precise measurements. In the life sciences, diamond-based quantum sensing has enabled a new class of biophysical sensors and diagnostic devices that are being investigated as a platform for cancer screening and ultra-sensitive immunoassays. However, a broader application in the life sciences based on nanoscale nuclear magnetic resonance spectroscopy has been hampered by the need to interface highly sensitive quantum bit (qubit) sensors with their biological targets. Here, we demonstrate a new approach that combines quantum engineering with single-molecule biophysics to immobilize individual proteins and DNA molecules on the surface of a bulk diamond crystal that hosts coherent nitrogen vacancy qubit sensors. Our thin (sub-5 nm) functionalization architecture provides precise control over protein adsorption density and results in near-surface qubit coherence approaching 100 {\mu}s. The developed architecture remains chemically stable under physiological conditions for over five days, making our technique compatible with most biophysical and biomedical applications.

Biocompatible surface functionalization architecture for a diamond quantum sensor

Quantum metrology enables some of the most precise measurements. In the life sciences, diamond-based quantum sensing has enabled a new class of biophysical sensors and diagnostic devices that are being investigated as a platform for cancer screening and ultra-sensitive immunoassays. However, a broader application in the life sciences based on nanoscale nuclear magnetic resonance spectroscopy has been hampered by the need to interface highly sensitive quantum bit (qubit) sensors with their biological targets. Here, we demonstrate a new approach that combines quantum engineering with single-molecule biophysics to immobilize individual proteins and DNA molecules on the surface of a bulk diamond crystal that hosts coherent nitrogen vacancy qubit sensors. Our thin (sub-5 nm) functionalization architecture provides precise control over protein adsorption density and results in near-surface qubit coherence approaching 100 {\mu}s. The developed architecture remains chemically stable under physiological conditions for over five days, making our technique compatible with most biophysical and biomedical applications. 

Diamond for antifouling applications: A review

Edge and defect sites in porous activated coke enable highly efficient carbon-assisted water electrolysis for energy-saving hydrogen production

Systematic comparison of various oxidation treatments on diamond surface

The surface functionalization of diamonds has been extensively studied through a variety of techniques, such as controlled oxidation. Several oxygen groups have been detected on oxidized diamonds, such as C–O–C (ester), C=O (ketonic), and C–OH (hydroxyl). However, the composition and relative concentration of these groups on diamond surfaces can be affected by the type of oxygenation treatment and the diamond surface quality. To investigate the stability of the oxygenated groups at specific diamond surfaces, we evaluated through fully atomistic reactive (ReaxFF force field) molecular mechanics (FARMM) simulations, the formation energies of the C=O, C–O–C, and C–OH groups on pristine and defective diamond surfaces (110), (111), and (311). According to our findings, the C–OH group has the lowest formation energy on a perfect (110) surface, while the C–O–C is favored on a defective surface. As for the (111) surface, the C–O–C group is the most stable for both pristine and defective surfaces. Similarly, C–O–C group is also the most stable one on the defective/perfect (311) surface. In this way, our results suggest that if, in a diamond film, the (110) surface is the major exposed facet, the most adsorbed oxygen group could be either C–OH or C–O–C, in which the C–O–C would depend on the level of surface defects. Graphical abstract

/pdf/stability-of-oxygenated-groups-on-pristine-and-defective-14igytk6.pdf

Stability of oxygenated groups on pristine and defective diamond surfaces

The surface functionalization of diamonds has been extensively studied through a variety of techniques, such as controlled oxidation. Several oxygen groups have been detected on oxidized diamonds, such as C–O–C (ester), C=O (ketonic), and C–OH (hydroxyl). However, the composition and relative concentration of these groups on diamond surfaces can be affected by the type of oxygenation treatment and the diamond surface quality. To investigate the stability of the oxygenated groups at specific diamond surfaces, we evaluated through fully atomistic reactive (ReaxFF force field) molecular mechanics (FARMM) simulations, the formation energies of the C=O, C–O–C, and C–OH groups on pristine and defective diamond surfaces (110), (111), and (311). According to our findings, the C–OH group has the lowest formation energy on a perfect (110) surface, while the C–O–C is favored on a defective surface. As for the (111) surface, the C–O–C group is the most stable for both pristine and defective surfaces. Similarly, C–O–C group is also the most stable one on the defective/perfect (311) surface. In this way, our results suggest that if, in a diamond film, the (110) surface is the major exposed facet, the most adsorbed oxygen group could be either C–OH or C–O–C, in which the C–O–C would depend on the level of surface defects.

/pdf/stability-of-oxygenated-groups-on-pristine-and-defective-17ssjlef.pdf

Seoyun Kong

Papers

Systematic comparison of various oxidation treatments on diamond surface

Stability of oxygenated groups on pristine and defective diamond surfaces

Stability of oxygenated groups on pristine and defective diamond surfaces