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

We report on the synthesis and the characterization of a new class of segmented polyethers POC containing the oxadiazole and carbazole units. The polymers exhibit a high thermal stability, high glass transition temperatures and good solubility in common organic solvents, despite the extended aromatic portion in the main polymer chain. According to previous reports on oxadiazole/carbazole containing materials, POC show high photoluminescence activity in the blue region of the visible spectra. The good solubility in chlorinate solvents allows the preparation of films with homogeneous thickness by spin coating. Glass transition temperature in the range 115–125° C ensures good stability of film morphology at room temperature. For these features, polymers POC are potential candidate materials for fabricating blue light emitting devices.

/pdf/synthesis-and-characterization-of-new-photoluminescent-1kmn7gsnga.pdf

Synthesis and Characterization of New Photoluminescent Oxadiazole/Carbazole Containing Polymers

In the last years the role of confinement in selecting conformations of polymers and in accelerating the convergence has been clearly stated. The choice of proper confining systems is crucial in designing new materials. In this contribution, the consequences of tailored mesostructures in controlling a series of physical‐mechanical‐electronical properties are discussed with a particular attention to magnetic materials and photonic crystals.

Design of novel polymeric materials by controlled self‐assembly

Photoresponsive biomaterials have garnered increasing attention recently due to their ability to dynamically regulate biological interactions and cellular behaviors in response to light. This review provides an overview of recent advances in the design, synthesis, and applications of photoresponsive biomaterials, including photochromic molecules, photocleavable linkers, and photoreactive polymers. We highlight the various approaches used to control the photoresponsive behavior of these materials, including modulation of light intensity, wavelength, and duration. Additionally, we discuss the applications of photoresponsive biomaterials in various fields, including drug delivery, tissue engineering, biosensing, and optical storage. A selection of significant cutting-edge articles collected in recent years has been discussed based on the structural pattern and light-responsive performance, focusing mainly on the photoactivity of azobenzene, hydrazone, diarylethenes, and spiropyrans, and the design of smart materials as the most targeted and desirable application. Overall, this review highlights the potential of photoresponsive biomaterials to enable spatiotemporal control of biological processes and opens up exciting opportunities for developing advanced biomaterials with enhanced functionality.

/pdf/recent-progress-in-photoresponsive-biomaterials-dmnndck2.pdf

Recent Progress in Photoresponsive Biomaterials

Antimicrobial peptides AMP are small proteins produced by the innate immune system in multicellular microorganisms. The mechanism of action of AMP on target membranes can be divided in two main categories: pore forming and non-pore forming mechanisms. We applied a computational approach to design novel linear peptides having high specificity and low toxicity against common pathogens. We built up QSAR models using the data present in a database of antimicrobial peptides. Here, we present new models of activities obtained by the use of evolutionary methods and the relative statistical validation.

Models for the Prediction of Antimicrobial Peptides Activity

Transcatheter Embolization, also called Embolotherapy, is a mini-invasive, non-surgical therapeutic solution used in Interventional Radiology to close blood vessels deliberately. A wide range of embolic agents is available in clinical practice, including metal coils and liquid agents. More recent advances in biomaterials such as shape-memory foam and in-situ gelling solutions have led to the development of new pre-clinical embolic agents. This review offers a brief overview of current and emerging technologies in the field of endovascular embolization. The focus is on devices, materials and techniques.

Simona Concilio

Papers

Synthesis and Characterization of New Photoluminescent Oxadiazole/Carbazole Containing Polymers

Design of novel polymeric materials by controlled self‐assembly

Recent Progress in Photoresponsive Biomaterials

Models for the Prediction of Antimicrobial Peptides Activity

Image-Guided Mini-Invasive Treatments for Vascular and Oncologic Diseases: Embolization Therapy