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

https://www.cell.com/trends/biotechnology/pdf/S0167-7799(05)00092-2.pdf

Microbial fuel cells: novel biotechnology for energy generation

https://cyberleninka.org/article/n/238598.pdf

Use of electrospinning technique for biomedical applications

Microbial fuel cells hold great promise as a sustainable biotechnological solution to future energy needs. Current efforts to improve the efficiency of such fuel cells are limited by the lack of knowledge about the microbial ecology of these systems. The purposes of this study were (i) to elucidate whether a bacterial community, either suspended or attached to an electrode, can evolve in a microbial fuel cell to bring about higher power output, and (ii) to identify species responsible for the electricity generation. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a biofuel cell in which glucose was used increased the output from an initial level of 0.6 W m−2 of electrode surface to a maximal level of 4.31 W m−2 (664 mV, 30.9 mA) when plain graphite electrodes were used. This result was obtained with an average loading rate of 1 g of glucose liter−1 day−1 and corresponded to 81% efficiency for electron transfer from glucose to electricity. Cyclic voltammetry indicated that the enhanced microbial consortium had either membrane-bound or excreted redox components that were not initially detected in the community. Dominant species of the enhanced culture were identified by denaturing gradient gel electrophoresis and culturing. The community consisted mainly of facultative anaerobic bacteria, such as Alcaligenes faecalis and Enterococcus gallinarum, which are capable of hydrogen production. Pseudomonas aeruginosa and other Pseudomonas species were also isolated. For several isolates, electrochemical activity was mainly due to excreted redox mediators, and one of these mediators, pyocyanin produced by P. aeruginosa, could be characterized. Overall, the enrichment procedure, irrespective of whether only attached or suspended bacteria were examined, selected for organisms capable of mediating the electron transfer either by direct bacterial transfer or by excretion of redox components.

https://espace.library.uq.edu.au/view/UQ:164735/UQ164735_OA.pdf

Biofuel Cells Select for Microbial Consortia That Self-Mediate Electron Transfer

Microbial fuel cells: From fundamentals to applications. A review

https://blogs.epfl.ch/biofuelcells/documents/Enzyme-based%20biofuel%20cells.pdf

Enzyme-based biofuel cells

Biofuel cells are energy conversion devices that use biocatalysts to convert chemical energy to electrical energy. Over the last decade, research in this area has intensified, especially in the area of direct electron transfer between enzymes and electrodes. This review details the fundamentals of enzymatic biofuel cells and reviews characterization techniques that can be used to evaluate and optimize biofuel cells. The review details the advantages and disadvantages of mediated and direct bioelectrocatalysis at electrodes for biofuel cells. It also compares and contrasts different enzyme immobilization techniques and different electrode structures.

Enzyme catalysed biofuel cells

A wide variety of terrestrial biomass feed stocks have been identified as suitable candidates for fractionation and conversion into biofuels. In particular, microalgae have been promoted as a future source of transportation fuels primarily because of their stated potential to produce up to 10 times more oil per acre than traditional biofuel crops. Their ability to grow relatively fast, be harvested on a daily basis, and grown in earthen ponds or closed photobioreactors that occupy marginal or poor crop lands using salt or brackish water, are often referenced. When these attractive traits are coupled with the potential to concomitantly harvest valuable co‐products such as biopolymers, proteins, and animal feeds, one can see why microalgae are often touted as biotechnology's “green gold”. The development of large‐scale microalgae farms, however, has been slowed by limitations in downstream processing technology. For example, traditional methods to dewater, extract, and recover bio‐oil from oil‐seeds possess...

Michael J. Cooney

Papers

Enzyme-based biofuel cells

Enzyme catalysed biofuel cells

Extraction of Bio-oils from Microalgae

Fluorescent measurement of microalgal neutral lipids.

Lipid extraction from biomass using co-solvent mixtures of ionic liquids and polar covalent molecules