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

This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).

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Cellulose nanomaterials review: structure, properties and nanocomposites

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

Cellulose constitutes the most abundant renewable polymer resource available today. As a chemical raw material, it is generally well-known that it has been used in the form of fibers or derivatives for nearly 150 years for a wide spectrum of products and materials in daily life. What has not been known until relatively recently is that when cellulose fibers are subjected to acid hydrolysis, the fibers yield defect-free, rod-like crystalline residues. Cellulose nanocrystals (CNs) have garnered in the materials community a tremendous level of attention that does not appear to be relenting. These biopolymeric assemblies warrant such attention not only because of their unsurpassed quintessential physical and chemical properties (as will become evident in the review) but also because of their inherent renewability and sustainability in addition to their abundance. They have been the subject of a wide array of research efforts as reinforcing agents in nanocomposites due to their low cost, availability, renewability, light weight, nanoscale dimension, and unique morphology. Indeed, CNs are the fundamental constitutive polymeric motifs of macroscopic cellulosic-based fibers whose sheer volume dwarfs any known natural or synthetic biomaterial. Biopolymers such as cellulose and lignin and † North Carolina State University. ‡ Helsinki University of Technology. Dr. Youssef Habibi is a research assistant professor at the Department of Forest Biomaterials at North Carolina State University. He received his Ph.D. in 2004 in organic chemistry from Joseph Fourier University (Grenoble, France) jointly with CERMAV (Centre de Recherche sur les Macromolecules Vegetales) and Cadi Ayyad University (Marrakesh, Morocco). During his Ph.D., he worked on the structural characterization of cell wall polysaccharides and also performed surface chemical modification, mainly TEMPO-mediated oxidation, of crystalline polysaccharides, as well as their nanocrystals. Prior to joining NCSU, he worked as assistant professor at the French Engineering School of Paper, Printing and Biomaterials (PAGORA, Grenoble Institute of Technology, France) on the development of biodegradable nanocomposites based on nanocrystalline polysaccharides. He also spent two years as postdoctoral fellow at the French Institute for Agricultural Research, INRA, where he developed new nanostructured thin films based on cellulose nanowiskers. Dr. Habibi’s research interests include the sustainable production of materials from biomass, development of high performance nanocomposites from lignocellulosic materials, biomass conversion technologies, and the application of novel analytical tools in biomass research. Chem. Rev. 2010, 110, 3479–3500 3479

Cellulose nanocrystals: chemistry, self-assembly, and applications.

Lignocellulosic biomass has long been recognized as a potential sustainable source of mixed sugars for fermentation to biofuels and other biomaterials. Several technologies have been developed during the past 80 years that allow this conversion process to occur, and the clear objective now is to make this process cost-competitive in today's markets. Here, we consider the natural resistance of plant cell walls to microbial and enzymatic deconstruction, collectively known as "biomass recalcitrance." It is this property of plants that is largely responsible for the high cost of lignocellulose conversion. To achieve sustainable energy production, it will be necessary to overcome the chemical and structural properties that have evolved in biomass to prevent its disassembly.

http://science.sciencemag.org/content/sci/315/5813/804.full.pdf

Biomass recalcitrance: engineering plants and enzymes for biofuels production.

Chemical action between cyclodextrins (CDs) and TOPO-(CdSe)ZnS quantum dots (QDs) generates a water-soluble solution of CD-QDs. Hydrophobic TOPO molecules on surface of the QDs are compatible to thread through the pockets of CDs and make the hydroxyl group on end of CDs to approach the ZnS surface, and then cause the interaction between ZnS and the hydroxyls. In this paper, Photoluminescence of the γ-CD-QD solution appeared about 15 nm of red movement compared with that of the QDs in hexane; 58% replacement of the crystal coordinate bond of Zn-S with that of Zn-O in the ZnS shell was demonstrated by using first-principles density functional theory and the red shift of the photoluminescence of CD-QDs; and–0.11eV of the energy gain of the exchange model was calculated by using an effective mass (EM) model. CD-QDs will provide water-soluble QDs with conjugational group for biology and molecule-device applications.

Cyclodextrins stabilize TOPO-(CdSe)ZnS quantum dots in water

Stabilization of (CdSe)ZnS quantum dots in water using amino acid capping groups

Single-molecule fluorescence detection is an invaluable technique for the study of molecular behavior in biological systems, both in vitro and in vivo. In this chapter, we focus on detailed protocols that utilize Total Internal Reflection Fluorescence Microscopy (TIRF-M) to visualize single molecules of carbohydrate-binding module (CBM) labeled with green fluorescent protein (GFP). The content describes step-by-step sample preparation and data acquisition, processing, and analysis. These methods can also be further used to study interactions between domains of cellulase molecules and between cellulases and cellulose.

Shi You Ding

Papers

Cyclodextrins stabilize TOPO-(CdSe)ZnS quantum dots in water

Stabilization of (CdSe)ZnS quantum dots in water using amino acid capping groups

Single-Molecule Tracking of Carbohydrate-Binding Modules on Cellulose Using Fluorescence Microscopy

Chapter 11: Bacterial Protein Complexes with Potential Applications in Nanotechnology

Overview of Lignocellulose: Structure and Chemistry