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

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

A review was presented to demonstrate a historical description of the synthesis of light-emitting conjugated polymers for applications in electroluminescent devices. Electroluminescence (EL) was first reported in poly(para-phenylene vinylene) (PPV) in 1990 and researchers continued to make significant efforts to develop conjugated materials as the active units in light-emitting devices (LED) to be used in display applications. Conjugated oligomers were used as luminescent materials and as models for conjugated polymers in the review. Oligomers were used to demonstrate a structure and property relationship to determine a key polymer property or to demonstrate a technique that was to be applied to polymers. The review focused on demonstrating the way polymer structures were made and the way their properties were controlled by intelligent and rational and synthetic design.

Synthesis of Light-Emitting Conjugated Polymers for Applications in Electroluminescent Devices

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

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

Donor−Acceptor-Substituted Phenylethenyl Bithiophenes: Highly Efficient and Stable Nonlinear Optical Chromophores

Chitosan (CH) is one of the polymers most frequently proposed in form of hydrogels for tissue engineering (TE) applications. It is often crosslinked with the aim of improving its stability and mechanical properties. In this work, a supercritical carbon dioxide (SC-CO2) gel drying process was proposed to obtain CH scaffolds and, for the first time, the simultaneous elimination of unreacted glutaraldehyde (GTA), taking advantage of its solubility in supercritical mixtures. SC-CO2 gel dried crosslinked CH aerogels showed a nanofibrous structure characterized by an average diameter of about 100 nm. No collapse of the nanostructure was observed in the aerogels, due to the peculiarities of supercritical fluids (e.g., near zero surface tension). Moreover, crosslinked CH showed a thermally stable structure, as determined by TGA analysis. The hypothesis that a supercritical mixture is able to efficiently extract GTA residues entrapped in the gel matrix was also verified: negligible residues of GTA were found at the end of release experiments; in particular, at the best operating conditions, a GTA concentration equal to 0.013 ppm was detected. Therefore, the produced crosslinked CH aerogels can be effectively and safely used for TE applications.

Complete glutaraldehyde elimination during chitosan hydrogel drying by SC-CO2 processing

Natural polymers, such as alginate and gelatin, can be used to produce scaffolds for tissue engineering applications; but, their mechanical and biochemical performance should be improved. A possible solution to obtain this result, is the generation of multi-component scaffolds, by blending two or more polymers. One way to realize it, is the formation of an interpenetrating polymer network (IPN). In this work, the interpenetration of alginate and gelatin hydrogels has been successfully obtained and preserved by supercritical CO2 (SC-CO2) drying performed at 200 bar and 35 °C, using different blend compositions: from alginate/gelatin = 20:80 v/v to alginate/gelatin = 80:20 v/v. The process allowed modulation of morphology and mechanical properties of these blends. The overall result was made possible by the supercritical drying process that, working at zero surface tension, allows preserving the hydrogels nanostructure in the corresponding aerogels.

/pdf/interpenetration-of-natural-polymer-aerogels-by-1gteq3dwg3.pdf

Simona Concilio

Papers

YADAMP: yet another database of antimicrobial peptides

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

Donor−Acceptor-Substituted Phenylethenyl Bithiophenes: Highly Efficient and Stable Nonlinear Optical Chromophores

Complete glutaraldehyde elimination during chitosan hydrogel drying by SC-CO2 processing

Interpenetration of Natural Polymer Aerogels by Supercritical Drying.