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

Light-Emitting Diodes. (Monographs in Electrical and Electronic Engineering.) By A. A. Bergh and P. J. Dean. Pp. viii+591. (Clarendon: Oxford; Oxford University: London, 1976.) £22.

/pdf/light-emitting-diodes-ubzde6g9qc.pdf

Light-emitting diodes

The antimicrobial peptide database (APD, http://aps.unmc.edu/AP/) is an original database initially online in 2003. The APD2 (2009 version) has been regularly updated and further expanded into the APD3. This database currently focuses on natural antimicrobial peptides (AMPs) with defined sequence and activity. It includes a total of 2619 AMPs with 261 bacteriocins from bacteria, 4 AMPs from archaea, 7 from protists, 13 from fungi, 321 from plants and 1972 animal host defense peptides. The APD3 contains 2169 antibacterial, 172 antiviral, 105 anti-HIV, 959 antifungal, 80 antiparasitic and 185 anticancer peptides. Newly annotated are AMPs with antibiofilm, antimalarial, anti-protist, insecticidal, spermicidal, chemotactic, wound healing, antioxidant and protease inhibiting properties. We also describe other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. Amino acid profiles or signatures of natural AMPs are important for peptide classification, prediction and design. Finally, we summarize various database applications in research and education.

APD3: the antimicrobial peptide database as a tool for research and education

Listeria monocytogenes is a Gram positive, aerobic, facultative anaerobic and nonacid fast bacterium, which can cause the disease listeriosis in both human and animals. It is widely distributed thoroughout the environment and has been isolated from various plant and animal food products associated with listeriosis outbreaks.

Contaminated ready-to-eat food products such as gravad and cold-smoked salmon and rainbow trout have been associated with human listeriosis in Sweden. The aim of this study was to analyse the occurrence and level of L. monocytogenes in
gravad and cold-smoked salmon (Salmo salar) products packed under vacuum or modified atmosphere from retail outlets in Sweden. Isolated strains were characterized by serotyping and the diversity of the strains within and between
producers were determined with PFGE (Pulsed-field gel electrophoresis). The characterized fish isolates were compared with previously characterized human strains.
L. monocytogenes was isolated from 11 (three manufacturers) of 56 products analysed. This included gravad salmon products from three manufacturers and cold-smoked salmon from one manufacturer. The highest level of L. monocytogenes found was 1500 cfu/g from a cold-smoked salmon product but the level was low (<100 cfu/g) in most of the products. Serovar 1/2a was predominant,
followed by 4b. Three products of gravad salmon harboured more than one serovar. PFGE typing of the 56 salmon isolates detected five Asc I types: four types were identical to human clinical strains with Asc I and one was identical and one was closely related to human clinical strains with Apa I. Isolation of identical or closely related L. monocytogenes strains from human clinical cases of listeriosis and gravad and cold-smoked salmon suggested that these kinds of products are possible sources of listeriosis in Sweden. Therefore, these products should be considered risk products for human listeriosis.

Listeria monocytogenes, a food-borne pathogen

Nanomaterials are finding increasing use for biomedical applications such as imaging, diagnostics, and drug delivery. While it is well understood that nanoparticle (NP) physico-chemical properties can dictate biological responses and interactions, it has been difficult to outline a unifying framework to directly link NP properties to expected in vitro and in vivo outcomes. When introduced to complex biological media containing electrolytes, proteins, lipids, etc., nanoparticles (NPs) are subjected to a range of forces which determine their behavior in this environment. One aspect of NP behavior in biological systems that is often understated or overlooked is aggregation. NP aggregation will significantly alter in vitro behavior (dosimetry, NP uptake, cytotoxicity), as well as in vivo fate (pharmacokinetics, toxicity, biodistribution). Thus, understanding the factors driving NP colloidal stability and aggregation is paramount. Furthermore, studying biological interactions with NPs at the nanoscale level requires an interdisciplinary effort with a robust understanding of multiple characterization techniques. This review examines the factors that determine NP colloidal stability, the various efforts to stabilize NP in biological media, the methods to characterize NP colloidal stability in situ, and provides a discussion regarding NP interactions with cells.

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Nanoparticle colloidal stability in cell culture media and impact on cellular interactions

YADAMP: yet another database of antimicrobial peptides

In this work, we studied energetic and optical proprieties of a polyester-containing oxadiazole and carbazole units that we will indicate as POC. This polymer is characterized by high photoluminescence activity in the blue region of the visible spectrum, making it suitable for the development of efficient white-emitting organic light emission devices. Moreover, POC polymer has been combined with two red emitters InP/ZnS quantum dots (QDs) to obtain nanocomposites with wide emission spectra. The two types of QDs have different absorption wavelengths: 570 nm [InP/ZnS(570)] and 627 nm [InP/ZnS(627)] and were inserted in the polymer at different concentrations. The optical properties of the nanocomposites have been investigated and compared to the ones of the pure polymer. Both spectral and time resolved fluorescence measurements show an efficient energy transfer from the polymer to QDs, resulting in white-emitting nanocomposites.

White light-emitting nanocomposites based on an oxadiazole–carbazole copolymer (POC) and InP/ZnS quantum dots

Some novel (phenyl-diazenyl)phenols (4a–m) were designed and synthesized to be evaluated for their antibacterial activity. Starting from an active previously-synthesized azobenzene chosen as lead compound, we introduced some modifications and optimization of the structure, in order to improve solubility and drug conveyance. Structures of all newly-synthesized compounds were confirmed by 1H nuclear magnetic resonance (NMR), mass spectrometry, and UV-Vis spectroscopy. Antibacterial activity of the new compounds was tested with the dilution method against the bacteria strains Listeria monocytogenes, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa PAO1. All the compounds were selectively active against Gram-positive bacteria. In particular, compounds 4d, 4h, and 4i showed the highest activity against S. aureus and Listeria monocytogenes, reaching remarkable MIC100 values of 4 μg/mL and 8 μg/mL. The relationship between antimicrobial activity and compound structure has suggested that the presence of hydroxyl groups seems to be essential for antimicrobial activity of phenolic compounds.

https://www.mdpi.com/1420-3049/22/8/1372/pdf

Synthesis and Antimicrobial Studies of New Antibacterial Azo-Compounds Active against Staphylococcus aureus and Listeria monocytogenes

Small azobenzene derivatives active against bacteria and fungi

Using solvent casting and melt compounding methods, we realized antibacterial and antifungal poly(lactic acid)-based films by introducing different percentages of antimicrobial azo dyes into polymer matrices. Concentration up to 0.01% (w/w) of azo compounds permitted the preparation of antimicrobial and transparent films. The thin films retained the properties of the pure PLA matrices, such as glass transition temperature, flexibility, and amorphous nature. The films exhibited antimicrobial activity and the capability to inhibit biofilms formation of Staphylococcus aureus and Candida albicans. Spectrophotometric investigation of azo compounds release from the polymer matrices confirmed that the materials might have applications in fields where an intrinsic antimicrobial ability of the material is required, such as biomedical tools, biodegradable antibacterial coatings, and films for active packaging. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42357.

Lucia Sessa

Papers

YADAMP: yet another database of antimicrobial peptides

White light-emitting nanocomposites based on an oxadiazole–carbazole copolymer (POC) and InP/ZnS quantum dots

Synthesis and Antimicrobial Studies of New Antibacterial Azo-Compounds Active against Staphylococcus aureus and Listeria monocytogenes

Small azobenzene derivatives active against bacteria and fungi

Biodegradable antimicrobial films based on poly(lactic acid) matrices and active azo compounds