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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
    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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  • 3
    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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  • 4
    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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  • 5
    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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  • 6
    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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  • 7
    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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  • 8
    Electronic Resource
    Electronic Resource
    Ground state of random copolymers and the discrete random energy model (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 98 (1993), S. 8174-8177 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We propose and investigate a modification of the random energy model where the energies of different states are still independent random values but may take only discrete values. This model appears naturally in studies of random heteropolymers with monomers of two types. We calculate the probability that the ground state of such a polymer is nondegenerate and test this result against a lattice model of a heteropolymer with exhaustively enumerated conformations. The theory is in excellent agreement with numerical experiment. Our results imply that the lower the energy of the ground state the less probable that it is degenerate. The probability of degeneracy decays exponentially as ground state energy decreases.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.464522
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  • 9
    Electronic Resource
    Electronic Resource
    Fluctuation effects on microphase separation in random copolymers (1994)
    Springer
    Il nuovo cimento della Società Italiana di Fisica 16 (1994), S. 879-882 
    Details
    ISSN: 0392-6737
    Keywords: Order-disorder and statistical mechanics of model systems ; Multicritical points ; Macromolecules and polymer molecules: Constitution (chains and sequences) ; Conference proceedings
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Summary We study random copolymers consisting of two kinds of monomers with attraction between similar kinds. The mean-field analysis of this system indicates a continuous phase transition into a phase with periodic microdomain structure. It is shown that the inverse of the renormalized propagator has a minimum at non-zero wave numbers. Consequently, there is an anomalously large contribution of fluctuations that make the disordered phase locally stable. However, below a certain temperature, the ordered phase is shown to be locally stable and a weak first-order transition is possible, with qualitative differences from the weak crystallization theory developed by Brazovskii. These differences are due to the peculiar form of the fourth-order vertex of the effective Hamiltonian for the system. We calculated the temperature region for the validity of the mean-field estimates of the amplitude and the scale of microphase separation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02456738
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  • 10
    Electronic Resource
    Electronic Resource
    Freezing and microphase separation in random copolymers (1994)
    Springer
    Il nuovo cimento della Società Italiana di Fisica 16 (1994), S. 873-877 
    Details
    ISSN: 0392-6737
    Keywords: Physical chemistry of solutions of biological macromolecules ; Order-disorder and statistical mechanics of model systems ; Multicritical points ; Macromolecules and polymer molecules: Constitution (chains and sequences) ; Conference proceedings
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Summary A two-letter random copolymer with attraction between similar monomers and repulsion between different ones is investigated using the replica method. This type of interactions favors microphase separation (MPS) in a compact state of a polymer or in a melt. Frustrations between interactions and polymeric bonds may lead to freezing transition in a phase where only a few conformations dominate and replica symmetry is broken. Our analysis reveals that stiff polymers have a frozen phase and do not undergo transition to a phase with microdomain structure. In flexible polymers the microphase transition may occur before freezing. A complete phase diagram showing the interplay between the two phase transitions is constructed for the two-letter random copolymer.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02456737
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