The ball-and-stick model of DNA 

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... ibm.com/developerWorks/ • A roundup of Blue Gene/L-related research can be found at the IBM Blue Gene project page. Other Blue Gene solution components and resources include: • The IBM Blue Gene/P solution page • The IBM General Parallel File System • Everything you could want to know about the IBM XL C/C++ Advanced Edition for Blue Gene compiler • IBM Redbooks on Blue Gene technologies • And a picture of the Blue Gene used by one of the authors • The RCSB Protein Data Bank (PDB) is an archive for the study of biological macromolecules with information about experimentally determined structures of proteins, nucleic acids, and complex assemblies. Educational resources include such cool things as the Molecule of the Month. • Source data for Figure 1 is from the PDB, The 1.33 A structure of tetragonal hen egg white lysozyme. • Source data for Figure 2 is from the PDB, Structure of a B-DNA dodecamer: conformation and dynamics. • Figure 3 is courtesy of the MathMol library hosted at New York University. • Source data for Figure 4 is from the PDB, Deoxy hemoglobin (A-GLY-C:V1M,L29F,H58Q; B,D:V1M,L106W). • Chris Dobson's group posts links to more research in molecular biology. • "Destruction of long-range interactions by a single mutation in lysozyme" (R. Zhou, M. Eleftheriou, A. Royyuru, B. J. Berne; Proc. Natl. Acad. Sci., 2007) gives more information about the modeling approach used in these simulations. • "Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L" (M. Eleftheriou, A. Rayshubski, J. W. Pitera, B. G. Fitch, R. Zhou, R. S. Germain; IEEE, 2006) explains some of the mathematical techniques used for the simulation. • MPICH2 is the next stage of MPICH, the high-performance, widely portable (and free) implementation of the Message Passing Interface (MPI) standard. • The Argonne Leadership Computing Facility has a collaborative program that provides Blue Gene/P time to the computational science community. • The modeling application is available for demonstration at IBM Innovation Centers worldwide. • "High-performance Linux clustering" is a two-part series providing background on high- performance computing with Linux. Part 1 (developerWorks, September 2005) covers HPC fundamentals, types of clusters available, reasons for choosing a cluster configuration, and the role of Linux in HPC. Part 2 (developerWorks, October 2005) discusses parallel programming using MPI, covers cluster management and benchmarking, and shows how to set up a Linux cluster using open source software. • "Port Fortran applications" (developerWorks, April 2009) helps you overcome common hurdles when porting Fortran applications among various high performance computing ...

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... are biological macromolecules that are an essential component of organisms and participate in every process within cells. Many proteins are enzymes that catalyze biochemical reactions; some are involved in cell signaling and immune responses; many others have structural and mechanical functions for muscles and cytoskeletons. Two examples illustrate how pervasive and important proteins are: • One protein is responsible for the "redness" of blood; it carries oxygen from the lungs to all the other parts of the body. • Another protein is responsible for the human body's response to the poison in poison-ivy; extremely irritating, but not normally harmful. There are hundreds of thousands of proteins involved in life on Earth. Proteomics is the study of how proteins work, how they interact, and how their diversity and specialization evolve among the living organisms around us. This article is a short tour of what proteins are, how they are made, and how they affect the systems they inhabit. DNA is the information storage component in every cell in every plant and animal. It stores information as a sequence of chemical building blocks (nucleotides) we call A , C , T , and G (for adenine, cytosine, thymine, and guanine in DNA, and uracil replacing thymine in RNA). From a distance, these building blocks look very similar, so every piece of DNA you look at has the same overall shape—the famous Watson-Crick Double Helix. To read out the information in the DNA, the DNA untwists and another molecule called RNA is formed by presentation of the internal pattern. Rather like pressing a key into putty, you now have an image of the key in the putty. This RNA molecule is next presented as a blueprint to the ribosome, a protein that behaves like an all-purpose factory. The ribosome reads the A/C/T/G code in groups of three, allowing us to derive a 64-letter "alphabet." Twenty of these "letters" correspond to amino acids, the building blocks for proteins. These amino acids come mainly from the food we eat (humans cannot synthesize all the amino acids we need and therefore must obtain the others, called "essential" amino acids, from food). Each amino acid has a "head" and a "tail." The ribosome finds the appropriate amino acid for each "letter" and assembles them head-to-tail in sequence; other "letters" indicate when to start and when to stop. The resulting linear sequence of amino acids is a newly minted protein molecule, formed precisely according to the code imprinted in the section of DNA that was used. Stresses and strains between the atoms in the protein molecule, interactions with the slightly salty water in the cell, and random vibrations that you would call heat then cause the protein molecule to "fold" into a characteristic shape. Protein molecules are quite stable; some of them can exist unchanged for hundreds of years and sustain temperatures of hundreds of degrees, which would kill the organism that made them. They stay roughly the way they are until they are denatured by strong chemicals, high pressure, heat or cold, or by becoming food for another living thing. The shape and the way it varies with time, temperature, and surrounding molecules determine what the protein molecule will do—whether it will transport oxygen, give you a poison-ivy allergy, or do any of the other things that can happen at that tiny scale. Figure 2 demonstrates the familiar ball-and-stick model of DNA (image is a stereo pair; see Resources for the image ...