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  • 1
    Electronic Resource
    Electronic Resource
    Is Burst Hydrophobic Collapse Necessary for Protein Folding? (1995)
    s.l. : American Chemical Society
    Biochemistry 34 (1995), S. 3066-3076 
    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/bi00009a038
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  • 2
    Electronic Resource
    Electronic Resource
    Random heteropolymers in layered fluids (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 2043-2047 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study a simple model of a random heteropolymer, without excluded volume, in layered fluid systems of the form (i) ABA or ABC, where A, B, C denote three immiscible fluids, (ii) AB+hard wall, (iii) ABABA... . The quenched randomness is contained in the affinities {ξj; j=1,2,...,N} of the N links of the chain with the different fluids: these affinities are taken as random independent variables. Case (i) may be of interest for the localization of proteins in membranes, and (ii) pertains to the adsorption onto a wall. Using a replica-symmetric theory with a Hartree variational procedure, we study the behavior of the chain as a function of temperature. Various transitions [localization in case (i), adsorption in (ii)] are then exhibited. In the periodic situation (iii), the quenched and annealed randomness lead to the same results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.459081
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  • 3
    Electronic Resource
    Electronic Resource
    Specific Nucleus as the Transition State for Protein Folding: Evidence from the Lattice Model (1994)
    s.l. : American Chemical Society
    Biochemistry 33 (1994), S. 10026-10036 
    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/bi00199a029
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  • 4
    Electronic Resource
    Electronic Resource
    Statistical mechanics of polymers with distance constraints (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 100 (1994), S. 5290-5293 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ensemble of polymer conformations satisfying some distance constraints is studied using the replica approach. Dependence of the number of such conformations on the number of constraints is obtained. Possible implications of these results for the physics of polymer gels and the problem of protein structure reconstruction from NMR are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.467193
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  • 5
    Electronic Resource
    Electronic Resource
    Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations (1994)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 101 (1994), S. 6052-6062 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The implications of thermodynamics of heteropolymers for their folding kinetics are formulated and discussed. The predictions are tested by Monte Carlo simulation of folding of a lattice model 36-monomer proteins at different temperatures. Using a simulated annealing procedure in sequence space, a number of sequences are designed which have sufficiently low energy in a given target conformation. This conformation plays a role of the native structure for the model proteins. The folding transition is found to be cooperative, and the nature of the free energy barrier is studied. At high temperature the barrier is entropic, and at low temperature it is mainly energetic. This can be explained by transformation of the early partly folded intermediate from the disordered state (belonging to the quasicontinuous part of the energy spectrum) at high temperature to the non-native low-energy frozen conformation at low temperature. The latter plays a role of an off-pathway trap. A parallel folding process has been detected at low temperature where direct folding competes with relaxation of the intermediate. The frozen intermediate must unfold to make it possible to form a folding nucleus, which is the prerequisite of subsequent fast descent to the native state.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.467320
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  • 6
    Electronic Resource
    Electronic Resource
    Phase behavior of random copolymers in quenched random media (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 10751-10763 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper, we consider the behavior of random heteropolymers in a quenched disordered medium. We develop a field theory and obtain a mean-field solution that allows for replica symmetry breaking. The presence of an external disorder leads to the formation of compact states; a homopolymeric effect. We compute the phase diagram for two classes of problems. First, we consider the situation wherein the bare heteropolymer prefers like segments to segregate, and second, we examine cases where the bare heteropolymer prefers unlike segments to mix. For the first class of systems, we find a phase diagram characterized by a replica symmetry broken phase that exists below a particular temperature. This temperature grows with the strength of the external disorder. In the second class of situations, the phase diagram is much richer. Here we find two replica symmetry broken phases with different patterns separated by a reentrant phase. The reentrant phase and one of the two replica symmetry broken phases are induced by interactions with the external disorder. The dependence of the location of the phase boundaries on the strength of the external disorder are elucidated. We discuss our results from a physical standpoint, and note the testable experimental consequences of our findings. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469861
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  • 7
    Electronic Resource
    Electronic Resource
    Polymers with annealed and quenched branchings belong to different universality classes (1993)
    s.l. : American Chemical Society
    Macromolecules 26 (1993), S. 1293-1295 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00058a016
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  • 8
    Electronic Resource
    Electronic Resource
    Microphase separation in randomly branched polymers (1993)
    s.l. : American Chemical Society
    Macromolecules 26 (1993), S. 3598-3600 
    Details
    ISSN: 1520-5835
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ma00066a018
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  • 9
    Electronic Resource
    Electronic Resource
    Stability study of icosahedral phases in diblock copolymer melt (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 7591-7611 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The stability of three possible icosahedral phases (called here vertex, edge, and face models, respectively) in a diblock copolymer melt is examined, with higher harmonics included in the density-wave mean field theory developed by Leibler. Two cases are examined: (1) diblock copolymer melt with constant coupling vertices, and (2) diblock copolymer melt with general coupling vertices in which, unlike all the previous studies on the effect of higher order harmonics in diblock copolymer melt, the calculation is performed exactly. We find that icosahedral phases are always metastable and the mean-field phase diagram of the diblock copolymer is unchanged. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.477381
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  • 10
    Electronic Resource
    Electronic Resource
    Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 6466-6483 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Monte Carlo simulation of model proteins on a cubic lattice are used to study the thermodynamics and kinetics of protein folding over a wide range of temperatures. Both random sequences and sequences designed to have a pronounced minimum of energy are examined. There is no indication in the kinetics of a "glass" transition at low temperature, i.e., below the temperature of the equilibrium folding transition, the kinetics of folding is described by the Arrhenius law at all temperatures that were examined. The folding kinetics is single-exponential in the whole range of studied temperatures for random sequences. The general implications of the temperature dependence of the folding rate are discussed and related to certain properties of the energy spectrum. The results obtained in the simulations are in qualitative disagreement with the conclusions of a theoretical analysis of protein folding kinetics based on certain kinetics assumptions introduced in the Random Energy Model. The origins of the discrepancies are analyzed and a simple phenomenological theory is presented to describe the temperature dependence of the folding time for random sequences. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476053
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