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 antibacterial action of silver is utilized in numerous consumer products and medical devices. Metallic silver, silver salts, and also silver nanoparticles are used for this purpose. The state of research on the effect of silver on bacteria, cells, and higher organisms is summarized. It can be concluded that the therapeutic window for silver is narrower than often assumed. However, the risks for humans and the environment are probably limited.

Silver as Antibacterial Agent: Ion, Nanoparticle, and Metal

https://material.karlov.mff.cuni.cz/people/janecek/studenti/FyzMetNano/Estrin_AM61_2013_782.pdf

Extreme grain refinement by severe plastic deformation: A wealth of challenging science

A review of the biomaterials technologies for infection-resistant surfaces.

Biofilm formation is a key virulence factor for a wide range of microorganisms that cause chronic infections. The multifactorial nature of biofilm development and drug tolerance imposes great challenges for the use of conventional antimicrobials and indicates the need for multi-targeted or combinatorial therapies. In this Review, we focus on current therapeutic strategies and those under development that target vital structural and functional traits of microbial biofilms and drug tolerance mechanisms, including the extracellular matrix and dormant cells. We emphasize strategies that are supported by in vivo or ex vivo studies, highlight emerging biofilm-targeting technologies and provide a rationale for multi-targeted therapies aimed at disrupting the complex biofilm microenvironment.

/pdf/targeting-microbial-biofilms-current-and-prospective-2br9buvtyz.pdf

Targeting microbial biofilms: current and prospective therapeutic strategies.

................................................................................................................. i Acknowledgments .................................................................................................. iii Declaration ............................................................................................................. v List of publications ................................................................................................. vi List of tables ........................................................................................................... xvi List of figures ......................................................................................................... xviii CHAPTER

Investigation of bacterial attachment patterns on micro-and nano-restricted surface topographies

Strontium-doped hardystonite plasma sprayed coatings with robust antimicrobial activity

Biosensors in Food Traceability and Quality

Broad spectrum antibacterial zinc oxide-reduced graphene oxide nanocomposite for water depollution

Abstract Almost every abiotic surface of a material is readily colonised by bacteria, algae, and fungi, contributing to the degradation processes of materials. Both biocorrosion and microbially influenced corrosion (MIC) refer to the interaction of microbial cells and their metabolic products, such as exopolymeric substances (EPS), with an abiotic surface. Therefore, biofouling and biodeterioration of manufactured goods have economic and environmental ramifications for the user to tackle or remove the issue. While MIC is typically applied to metallic materials, newly developed and evolving materials frequently succumb to the effects of corrosion, resulting in a range of chemical reactions and transport mechanisms occurring in the material. Recent research on biocorrosion and biofouling of conventional and novel materials is discussed in this paper, showcasing the current knowledge regarding microbial and material interactions that contribute to biocorrosion and biofouling, including biofilms, anaerobic and aerobic environments, microbial assault, and the various roles microorganisms’ play. Additionally, we show the latest analytical techniques used to characterise and identify MIC on materials using a borescope, thermal imaging, Fourier transform infrared (FTIR), atomic force microscopy (AFM), scanning electron microscopy (SEM), X-ray photoelectron microscopy (XPS), X-ray diffraction (XRD), optical and epifluorescence microscopy, electrochemical impedance spectroscopy, and mass spectrometry, and chemometrics. 

/pdf/analytical-characterisation-of-material-corrosion-by-2uj5orx0.pdf

Vi Khanh Truong

Papers

Investigation of bacterial attachment patterns on micro-and nano-restricted surface topographies

Strontium-doped hardystonite plasma sprayed coatings with robust antimicrobial activity

Biosensors in Food Traceability and Quality

Broad spectrum antibacterial zinc oxide-reduced graphene oxide nanocomposite for water depollution

Analytical Characterisation of Material Corrosion by Biofilms