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  • 1
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    Bounds on reachable sets using ordinary differential equations with linear programs embedded (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-06
    Description: This work considers the computation of rigorous componentwise time-varying bounds on the states of a non-linear control system. This work develops a new implementation of an existing bounding theory that exploits physical information to produce tight bounds. It is shown that the solution of a certain initial value problem in ordinary differential equations (ODEs) depending on parametric linear programs (LPs) (which are said to be ‘embedded’) yields componentwise bounds. To ensure the numerical tractability of such a formulation, some properties of the resulting system of ODEs with LPs embedded are discussed. Finally, the tightness of the bounds are demonstrated for models of reacting chemical systems with uncertain rate parameters.
    Print ISSN: 0265-0754
    Electronic ISSN: 1471-6887
    Topics: Mathematics
    Published by Oxford University Press
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  • 2
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    Electron transfer between bases in double helical DNA (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-15
    Description: Fluorescent analogs of adenine that selectively oxidize guanine were used to investigate photoinduced electron transfer through the DNA pi-stack as a function of reactant stacking and energetics. Small variations in these factors led to profound changes in the kinetics and distance dependences of DNA-mediated electron-transfer reactions. Values of beta, a parameter reflecting the dependence of electron transfer on distance, ranged from 0.1 to 1.0 per angstrom. Strong stacking interactions result in the fastest electron-transfer kinetics. Electrons are thus transported preferentially through an intrastrand rather than interstrand pathway. Reactant energetics also modulate the distance dependence of DNA-mediated charge transport. These studies may resolve the range of disparate results previously reported, and paradigms must now be developed to describe these properties of the DNA pi-stack, which can range from insulator- to "wire"-like.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelley, S O -- Barton, J K -- GM49216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1999 Jan 15;283(5400):375-81.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beckman Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9888851" target="_blank"〉PubMed〈/a〉
    Keywords: 2-Aminopurine/chemistry ; Adenine/analogs & derivatives/chemistry ; Base Pairing ; DNA/*chemistry ; *Electrons ; Guanine/chemistry ; Hydrogen Bonding ; Kinetics ; Light ; Nucleic Acid Conformation ; Oxidation-Reduction ; Spectrometry, Fluorescence ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Accelerated electron transfer between metal complexes mediated by DNA (1988)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1988-09-23
    Description: DNA-mediated long-range electron transfer from photoexcited 1,10-phenanthroline complexes of ruthenium, Ru(phen)2(3)+, to isostructural complexes of cobalt(III), rhodium(III), and chromium(III) bound along the helical strand. The efficiency of transfer depended upon binding mode and driving force. For a given donor-acceptor pair, surface-bound complexes showed greater rate enhancements than those that were intercalatively bound. Even in rigid glycerol at 253 K, the rates for donor-acceptor pairs bound to DNA remained enhanced. For the series of acceptors, the greatest enhancement in electron-transfer rate was found with chromium, the acceptor of intermediate driving force. The DNA polymer appears to provide an efficient intervening medium to couple donor and acceptor metal complexes for electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Purugganan, M D -- Kumar, C V -- Turro, N J -- Barton, J K -- New York, N.Y. -- Science. 1988 Sep 23;241(4873):1645-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Columbia University, New York, NY 10027.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3420416" target="_blank"〉PubMed〈/a〉
    Keywords: Binding, Competitive ; DNA/*metabolism ; Diffusion ; Electron Transport ; Glycerol/metabolism ; Metals/*metabolism ; Models, Molecular ; Phenanthrolines/metabolism ; Ruthenium/metabolism ; Temperature ; Viscosity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Oxidative thymine dimer repair in the DNA helix (1997)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1997-03-07
    Description: The metallointercalator Rh(phi)2DMB3+ (phi, 9,10-phenanthrenequinone diimine; DMB, 4,4'-dimethyl-2,2'-bipyridine) catalyzed the repair of a thymine dimer incorporated site-specifically in a 16-base pair DNA duplex by means of visible light. This repair could be accomplished with rhodium noncovalently bound to the duplex and at long range (16 to 26 angstroms), with the rhodium intercalator tethered to either end of the duplex assembly. This long-range repair was mediated by the DNA helix. Repair efficiency did not decrease with increasing distance between intercalated rhodium and the thymine dimer, but it diminished with disruption of the intervening pi-stack.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dandliker, P J -- Holmlin, R E -- Barton, J K -- GM49216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1997 Mar 7;275(5305):1465-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9045609" target="_blank"〉PubMed〈/a〉
    Keywords: 2,2'-Dipyridyl/analogs & derivatives/metabolism ; Base Composition ; DNA/chemistry/*metabolism ; DNA Damage ; *DNA Repair ; Electron Transport ; Electrons ; Intercalating Agents/*metabolism ; Light ; *Nucleic Acid Conformation ; Organometallic Compounds/*metabolism ; Oxidation-Reduction ; Pyrimidine Dimers/*metabolism ; Rhodium/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Long-range photoinduced electron transfer through a DNA helix (1993)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1993-11-12
    Description: Rapid photoinduced electron transfer is demonstrated over a distance of greater than 40 angstroms between metallointercalators that are tethered to the 5' termini of a 15-base pair DNA duplex. An oligomeric assembly was synthesized in which the donor is Ru(phen)2dppz2+ (phen, phenanthroline, and dppz, dipyridophenazine) and the acceptor is Rh(phi)2phen3+ (phi, phenanthrenequinone diimine). These metal complexes are intercalated either one or two base steps in from the helix termini. Although the ruthenium-modified oligonucleotide hybridized to an unmodified complement luminesces intensely, the ruthenium-modified oligomer hybridized to the rhodium-modified oligomer shows no detectable luminescence. Time-resolved studies point to a lower limit of 10(9) per second for the quenching rate. No quenching was observed upon metallation of two complementary octamers by Ru(phen)3(2+) and Rh(phen)3(3+) under conditions where the phen complexes do not intercalate. The stacked aromatic heterocycles of the DNA duplex therefore serve as an efficient medium for coupling electron donors and acceptors over very long distances.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Murphy, C J -- Arkin, M R -- Jenkins, Y -- Ghatlia, N D -- Bossmann, S H -- Turro, N J -- Barton, J K -- GM49216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1993 Nov 12;262(5136):1025-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beckman Institute, California Institute of Technology, Pasadena 91125.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7802858" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; DNA/*chemistry ; *Electrons ; Intercalating Agents/*chemistry ; Lasers ; Luminescence ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/*chemistry ; Organometallic Compounds/chemistry ; Phenanthrenes/chemistry ; Phenanthrolines/chemistry ; Photochemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Rates of DNA-mediated electron transfer between metallointercalators (1996)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1996-07-26
    Description: Ultrafast emission and absorption spectroscopies were used to measure the kinetics of DNA-mediated electron transfer reactions between metal complexes intercalated into DNA. In the presence of rhodium(III) acceptor, a substantial fraction of photoexcited donor exhibits fast oxidative quenching (〉3 x 10(10) per second). Transient-absorption experiments indicate that, for a series of donors, the majority of back electron transfer is also very fast (approximately 10(10) per second). This rate is independent of the loading of acceptors on the helix, but is sensitive to sequence and pi stacking. The cooperative binding of donor and acceptor is considered unlikely on the basis of structural models and DNA photocleavage studies of binding. These data show that the DNA double helix differs significantly from proteins as a bridge for electron transfer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arkin, M R -- Stemp, E D -- Holmlin, R E -- Barton, J K -- Hormann, A -- Olson, E J -- Barbara, P F -- GM49216/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1996 Jul 26;273(5274):475-80.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/8662532" target="_blank"〉PubMed〈/a〉
    Keywords: Chemistry, Physical ; DNA/*chemistry/*metabolism ; Electron Transport ; Intercalating Agents/chemistry/*metabolism ; Ligands ; *Nucleic Acid Conformation ; Organometallic Compounds/chemistry/*metabolism ; Photochemistry ; Physicochemical Phenomena ; Rhodium/metabolism ; Spectrum Analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    Binding of cis- and trans-dichlorodiammineplatinum(II) to DNA: evidence for unwinding and shortening of the double helix (1979)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1979-03-09
    Description: The antitumor drug cis-dichlorodiammineplatinum(II) (cis-DDP) and the inactive trans isomer bind and produce cooperative changes in closed and nicked circular duplex DNA's. Covalent binding of both platinum complexes to the closed circular DNA alters the degree of supercoiling, presumably by disrupting and unwinding the double helix. Electron micrographs show the platinated DNA's to be shortened by up to 50 percent of their original length. At similar ratios of bound platinum per nucleotide, the electrophoretic mobilities of the DNA's in gels containing the dye ethidium bromide are the same for both isomers. The only detectable difference in the binding of the two platinum isomers is an increase in the electrophoretic mobility in nondye gels of closed circular DNA having small amounts of bound cis-DDP that is not apparent for the trans complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, G L -- Bauer, W R -- Barton, J K -- Lippard, S J -- New York, N.Y. -- Science. 1979 Mar 9;203(4384):1014-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/370979" target="_blank"〉PubMed〈/a〉
    Keywords: Cisplatin/*metabolism/pharmacology ; DNA/*metabolism ; DNA, Circular/metabolism ; DNA, Superhelical/metabolism ; Electrophoresis ; Escherichia coli ; Isomerism ; Nucleic Acid Conformation/drug effects ; Plasmids
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Metals and DNA: molecular left-handed complements (1986)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1986-08-15
    Description: Chiral metal complexes provide unique molecular probes for DNA. Chiral reagents that "recognize" different local structures along the DNA strand have been designed by a process in which the asymmetry in shape and size of the complex is matched to that of the DNA helical groove. As a result, the chiral metal complexes provide very sensitive probes for local helical structure, both left- and right-handed. Direct coordination of chiral complexes to the DNA bases adds an element of sequence selectivity to the probe design. With a suitable reactive metal center, reagents that target chemically specific sites along the strand may be developed. One such chiral reagent, which cleaves left-handed DNA sites with photoactivation, has been useful in mapping this distinct conformation and examining its biological role. The conformation-specific molecular cleaver, much like a DNA-binding enzyme, recognizes and reacts at discrete sites along the DNA strand. These site-specific chiral metal complexes provide exciting new tools for probing the local variations in DNA structure and its role in the regulation of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barton, J K -- GM33309/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Aug 15;233(4765):727-34.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3016894" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; *DNA/genetics ; Genes, Regulator ; Intercalating Agents ; *Metals ; Models, Molecular ; *Nucleic Acid Conformation ; Plasmids ; RNA, Messenger/genetics ; Ruthenium ; Simian virus 40/genetics ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Electronic Resource
    Electronic Resource
    The 2-butyl cation in trifluoroacetic acid. A hydrogen-bridged carbonium ion (1981)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 103 (1981), S. 7764-7768 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00416a012
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  • 10
    Electronic Resource
    Electronic Resource
    Trifluoroacetolysis of optically active 2-butyl tosylate (1983)
    s.l. : American Chemical Society
    The @journal of organic chemistry 48 (1983), S. 4524-4527 
    Details
    ISSN: 1520-6904
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/jo00172a016
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