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 boundary layer equations for plane, incompressible, and steady flow are 

$$\matrix{ {u{{\partial u} \over {\partial x}} + v{{\partial u} \over {\partial y}} = - {1 \over \varrho }{{\partial p} \over {\partial x}} + v{{{\partial ^2}u} \over {\partial {y^2}}},} \cr {0 = {{\partial p} \over {\partial y}},} \cr {{{\partial u} \over {\partial x}} + {{\partial v} \over {\partial y}} = 0.} \cr }$$

Boundary Layer Theory

Fouling in membrane bioreactors used in wastewater treatment

Recent advances in membrane bioreactors (MBRs): membrane fouling and membrane material.

The stability of two-dimensional (2D) layers and membranes is subject of a long standing theoretical debate. According to the so called Mermin-Wagner theorem, long wavelength fluctuations destroy the long-range order for 2D crystals. Similarly, 2D membranes embedded in a 3D space have a tendency to be crumpled. These dangerous fluctuations can, however, be suppressed by anharmonic coupling between bending and stretching modes making that a two-dimensional membrane can exist but should present strong height fluctuations. The discovery of graphene, the first truly 2D crystal and the recent experimental observation of ripples in freely hanging graphene makes these issues especially important. Beside the academic interest, understanding the mechanisms of stability of graphene is crucial for understanding electronic transport in this material that is attracting so much interest for its unusual Dirac spectrum and electronic properties. Here we address the nature of these height fluctuations by means of straightforward atomistic Monte Carlo simulations based on a very accurate many-body interatomic potential for carbon. We find that ripples spontaneously appear due to thermal fluctuations with a size distribution peaked around 70 \AA which is compatible with experimental findings (50-100 \AA) but not with the current understanding of stability of flexible membranes. This unexpected result seems to be due to the multiplicity of chemical bonding in carbon.

Intrinsic ripples in graphene

A Molecular Dynamics Study Employing Bimetallic Co–Cuhab Nanosheets for Seawater Desalination

An experimental study was conducted to investigate the velocity characteristics of inclined gravity plumes. Two slope angles, 20 and 40 degrees, were examined. The velocity measurements were performed with Digital Particle Image Velocimetry through a proper matching of the refractive index of the effluent and the ambient water. The simulations were conducted in an inverted manner to reduce the amount of ethanol required for the refractive index matching. Results show that the centerline U-velocity profiles in the free mixing region follows a similarity curve after approximately 30d. The normal spreading of the plume increase when the slope increases. On the other hand, a wider lateral spread occurs when the sloping angle decreases.

Inverted simulation of gravity plumes

Surface wave measurements with IoT image processing

In the present study, we developed viscoelastic bottom layers of required rheological properties in the laboratory using a mixture of a polymer, polydimethylsiloxane with glycerol. The properties of the viscoelastic layers were quantified using oscillatory shear tests in a rheometer. Wave flume experiments with different viscoelastic bottom layers were then conducted under shallow water conditions. The synchronized time series data at seven locations along the direction of wave propagation were obtained using ultrasound sensors, which were used to determine the attenuation rate due to the presence of the bottom boundary. The results of the analysis showed that the attenuation rate of waves change with the variation of rheological property of bottom boundary, with the softer bottom attenuating the waves more significantly.

An Experimental Study on Surface Wave Modulation Due to Viscoelastic Bottom

Recently, remote sensing using survey-grade UAVs has been gaining tremendous momentum in applications for the coastal hydro-environment. UAV-based remote sensing provides high spatial and temporal resolutions and flexible operational availability compared to other means, such as satellite imagery or point-based in situ measurements. As strict requirements and government regulations are imposed for every UAV survey, detailed survey planning is essential to ensure safe operations and seamless coordination with other activities. This study established a comprehensive framework for the planning of efficient UAV deployments in coastal areas, which was based on recent on-site survey experiences with a portable unmanned aerial vehicle (pUAV) that was carrying a heavyweight spectral sensor. The framework was classified into three main categories: (i) pre-survey considerations (i.e., administrative preparation and UAV airframe details); (ii) execution strategies (i.e., parameters and contingency planning); and (iii) environmental effects (i.e., weather and marine conditions). The implementation and verification of the framework were performed using a UAV–airborne spectral sensing exercise for water quality monitoring in Singapore. The encountered challenges and the mitigation practices that were developed from the actual field experiences were integrated into the framework to advance the ease of UAV deployment for coastal monitoring and improve the acquisition process of high-quality remote sensing images.

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Adrian Wing-Keung Law

Papers

A Molecular Dynamics Study Employing Bimetallic Co–Cuhab Nanosheets for Seawater Desalination

Inverted simulation of gravity plumes

Surface wave measurements with IoT image processing

An Experimental Study on Surface Wave Modulation Due to Viscoelastic Bottom

A Framework for Survey Planning Using Portable Unmanned Aerial Vehicles (pUAVs) in Coastal Hydro-Environment