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  • 1
    Electronic Resource
    Electronic Resource
    Fluorescence Labeling of the Palmitoylation Sites of Rhodopsin (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 5783-5790 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00185a016
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  • 2
    Electronic Resource
    Electronic Resource
    Effects of Depalmitoylation on Physicochemical Properties of Rhodopsin (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 1718-1723 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00173a014
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  • 3
    Electronic Resource
    Electronic Resource
    Room Temperature Trapping of Rhodopsin Photointermediates (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 4454-4459 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00181a004
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  • 4
    Electronic Resource
    Electronic Resource
    Fluorescence Studies of the Location and Membrane Accessibility of the Palmitoylation Sites of Rhodopsin (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 5791-5796 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00185a017
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  • 5
    Electronic Resource
    Electronic Resource
    Fluorescence resonance energy transfer on fractals (1992)
    s.l. : American Chemical Society
    Accounts of chemical research 25 (1992), S. 195-200 
    Details
    ISSN: 1520-4898
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ar00016a004
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  • 6
    Electronic Resource
    Electronic Resource
    Order–disorder transitions in finite biopolymers: A sequence generating function approach (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 7648-7653 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: While there are a number of techniques for evaluating partition functions describing helix–coil transitions in infinite biopolymers, few exact techniques exist for the finite polymer problem. In this work, the sequence generating function formalism is extended to allow the treatment of finite length biopolymers. This is achieved by representing the partition function generating function as an expansion that uses a descending series rather than an ascending series. In this formalism the partition function is directly determined by a contour integral that can be evaluated exactly by the calculus of residues. This exact evaluation has advantages over previously used steepest descent methods as it allows finite biopolymers to be treated. With this technique, order–disorder transitions in a nucleic acid double helix model are reexamined. The problem of the perfectly matched double helix is treated exactly. The finite case of this model requires that the roots of a trinomial equation be obtained. This equation is solved and it is shown that each root differs only by a phase factor. Thus, the roots are distributed about a circle in the complex plane. Yang–Lee theory is used to explore conditions under which first-order phase transitions will occur in these systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466857
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  • 7
    Electronic Resource
    Electronic Resource
    Stochastic complexity and statistical mechanics (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 10118-10125 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A statistical mechanical formalism based on stochastic complexity is presented. Stochastic complexity is a statistical estimation scheme that uses the principle of minimal description length (MDL). The basic concept is that the best form of statistical estimation is one in which both the data and the model's structure and parameters are represented in the shortest binary string. This scheme is a generalization that encompasses both the maximum likelihood and maximum entropy methods. To apply this scheme to thermodynamic systems, the minimal number of bits required to describe both the observables and the phase space coordinates of the system is determined. The entropy of a microcanonical ensemble is associated with this minimum description length. This formulation provides a means for calculating partition functions for nonequilibrium systems that are strongly nonergodic. Because of the Bayesian properties of this estimation scheme, techniques for "image reconstruction" of phase space can be developed. These allow partition functions to be calculated from computer simulation data. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477704
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  • 8
    Electronic Resource
    Electronic Resource
    Protein structure and polymer collapse (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 98 (1993), S. 2250-2257 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Scaling relationships and a self-consistent field (SCF) theory of the structure of globular proteins are presented. A large data base is examined which shows that the radius of gyration of a protein Rg scales as Nν, where ν is approximately 1/3. This scaling behavior is predicted for collapsed polymers. Additional justification for polymer collapse conditions is given by an analysis of the fractal dimension of protein backbones. A collection of data also shows that the surface area of proteins S scales as S ∼ Rdsg, where ds equals 2.1. This property is also shown to be consistent with polymer collapse. A detailed SCF theory is presented for a collapsed polymer in which two- and three-body interactions between the segments are considered. The problem is exactly solvable within the SCF level of approximation and analytic solutions are obtained for the configurational distribution function. The distribution function is used to calculate scaling relationships and the free energy of the polymer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.464205
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  • 9
    Electronic Resource
    Electronic Resource
    The Genotypic Landscape During In Vitro Evolution of a Catalytic RNA: Implications for Phenotypic Buffering (2000)
    Springer
    Journal of molecular evolution 50 (2000), S. 481-490 
    Details
    ISSN: 1432-1432
    Keywords: Key words: In vitro evolution — Selection-amplification methodology — Adaptive walks on rugged landscapes — Genotype–phenotype interactions.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The Tetrahymena group I ribozyme catalyzes the cleavage of a phosphodiester linkage in specific sequences of RNA. This phenotype can be used in an in vitro selection-amplification process to evolve variants that are capable of RNA catalysis in the presence of Ca2+ as the sole available cation. With sufficient genotypic characterization of the population as it evolves, we have a rare opportunity of observing how the information stored in an evolving population responds to selective pressures, such as the requisite of catalyzing RNA cleavage in the absence of Mg2+ or Mn2+. In the present work, we examine the population dynamics of this system using sequence information from previous experimental work. We focus on two issues: How does the information content of the population evolve? and Is the system evolving as an adaptive walk on a rugged landscape? To investigate these questions, information theoretical parameters are examined. The evolution of the population is visualized by mapping the genotypic frequency distribution onto a two-dimensional projection of sequence space. The projection was generated using Hamming distances from the wild-type, starting sequence and a catalytically successful, evolved sequence. The evolution of the information content of the system was measured by calculating the grammar complexity of the observed sequences, which showed a very slight increase over 12 generations. This result is consistent with the system performing a search for a local optimum. The dynamics of the population in this sequence space is consistent with an adaptive walk on an uncorrelated, or ``rugged,'' genotypic landscape, despite the observation that the phenotypic progress of the population appears smooth. The relative insensitivity of the phenotypic landscape to the variegation of the genotypic landscape suggests that the former is buffered against variation in the latter through various epigenetic-like mechanisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002390010051
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  • 10
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    Statistical mechanics of protein sequences (1999)
    American Physical Society
    Details
    Publication Date: 1999-10-01
    Print ISSN: 1063-651X
    Electronic ISSN: 1095-3787
    Topics: Physics
    Published by American Physical Society
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