Talk:PlanetPhysics/DNA Molecular Models

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%%% This file is part of PlanetPhysics snapshot of 2011-09-01 %%% Primary Title: DNA molecular models %%% Primary Category Code: 00. %%% Filename: DNAMolecularModels.tex %%% Version: 8 %%% Owner: bci1 %%% Author(s): bci1 %%% PlanetPhysics is released under the GNU Free Documentation License. %%% You should have received a file called fdl.txt along with this file. %%% If not, please write to gnu@gnu.org. \documentclass[12pt]{article} \pagestyle{empty} \setlength{\paperwidth}{8.5in} \setlength{\paperheight}{11in}

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\section{DNA molecular models:} \emph{\htmladdnormallink{molecular models}{http://planetphysics.us/encyclopedia/BesselFunctionsApplicationsToDiffractionByHelicalStructures.html} of DNA structures} are \htmladdnormallink{representations}{http://planetphysics.us/encyclopedia/CategoricalGroupRepresentation.html} of the molecular geometry and topology of Deoxyribonucleic acid (DNA) \htmladdnormallink{molecules}{http://planetphysics.us/encyclopedia/Molecule.html} using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for 'skeletal models', graphic \htmladdnormallink{computations}{http://planetphysics.us/encyclopedia/LQG2.html} and animations by \htmladdnormallink{computers}{http://planetphysics.us/encyclopedia/SupercomputerArchitercture.html}, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and \htmladdnormallink{molecular dynamics simulations}{http://planetphysics.us/encyclopedia/CurrentDensityInPlasma.html} that are very important for understanding how DNA \htmladdnormallink{functions}{http://planetphysics.us/encyclopedia/Bijective.html} in vivo. Thus, an old standing \htmladdnormallink{dynamic}{http://planetphysics.us/encyclopedia/MathematicalFoundationsOfQuantumTheories.html} problem is how DNA "self-replication" takes place in living cells that should involve transient uncoiling of supercoiled DNA fibers. Altough DNA consists of relatively rigid, very large elongated biopolymer molecules called "fibers" or chains (that are made of repeating nucleotide units of four basic \htmladdnormallink{types}{http://planetphysics.us/encyclopedia/Bijective.html}, attached to deoxyribose and phospate \htmladdnormallink{groups}{http://planetphysics.us/encyclopedia/TrivialGroupoid.html}), its molecular stucture in vivo undergoes dynamic configuration changes that involve dynamically attached water molecules and ions. Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve in vivo DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists. Like other large molecules and biopolymers, DNA often exists in multiple stable geometries (that is, it exhibits conformational isomerism) and configurational, quantum states which are close to each other in \htmladdnormallink{energy}{http://planetphysics.us/encyclopedia/CosmologicalConstant.html} on the potential energy surface of the DNA molecule. Such geometries can also be computed, at least in principle, by employing ab initio quantum chemistry methods that have high accuracy for small molecules. Such \htmladdnormallink{quantum geometries}{http://planetphysics.us/encyclopedia/NAQAT2.html} define an important class of ab initio molecular models of DNA whose exploration has barely started.

In an interesting twist of roles, the DNA molecule itself was proposed to be utilized for quantum computing. Both DNA nanostructures as well as DNA 'computing' biochips have been built. The more advanced, computer-based molecular models of DNA involve molecular dynamics simulations as well as quantum mechanical computations of vibro-rotations, delocalized \htmladdnormallink{molecular orbitals}{http://planetphysics.us/encyclopedia/MolecularOrbitals.html} (MOs), \htmladdnormallink{electric dipole}{http://planetphysics.us/encyclopedia/FluorescenceCrossCorrelationSpectroscopy.html} moments, hydrogen-bonding, and so on.

\subsection{Contents} 1 Importance 2 Examples of DNA molecular models 3 Images for DNA Structure Determination from \htmladdnormallink{X-ray}{http://planetphysics.us/encyclopedia/FluorescenceCrossCorrelationSpectroscopy.html} Patterns 4 Paracrystalline lattice models of B-DNA structures 5 Genomic and Biotechnology Applications of DNA molecular modeling 5.1 Gallery: DNA Molecular modeling applications 6 Databases for DNA molecular models and sequences 6.1 \htmladdnormallink{X-ray diffraction}{http://planetphysics.us/encyclopedia/LaserProducedPlasma.html} 6.2 \htmladdnormallink{neutron}{http://planetphysics.us/encyclopedia/Pions.html} scattering 6.3 X-ray microscopy 6.4 \htmladdnormallink{electron microscopy}{http://planetphysics.us/encyclopedia/ImageReconstructionByDoubleFT.html} 6.5 Atomic Force Microscopy (AFM) 6.5.1 Gallery of AFM Images 6.6 \htmladdnormallink{mass}{http://planetphysics.us/encyclopedia/CosmologicalConstant.html} spectrometry--Maldi informatics 6.7 Spectroscopy 6.8 Gallery: CARS (\htmladdnormallink{Raman}{http://planetphysics.us/encyclopedia/FluorescenceCrossCorrelationSpectroscopy.html} spectroscopy), Fluorescence \htmladdnormallink{confocal microscopy}{http://planetphysics.us/encyclopedia/SuperimposedConfocalImages.html}, and \htmladdnormallink{Hyperspectral Imaging}{http://planetphysics.us/encyclopedia/SpectralImaging.html} 6.9 Genomic and structural databases 7 Notes 8 References 9 See also 10 External links

{\bf Note:} This topic is based upon \htmladdnormallink{a GNUL entry and exchange protocols with an external website}{http://en.wikipedia.org/wiki/Molecular_models_of_DNA} that has advanced graphics and gallery imaging capabilities. A \htmladdnormallink{related exposition entry}{http://planetphysics.org/?op=getobj&from=lec&id=205} with GNUL based free encyclopedia downloads of the image galleries is also available at PlanetPhysics.org.

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