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  • 1
    Electronic Resource
    Electronic Resource
    Freezing in polyampholytes globules: Influence of the long-range nature of the interaction (1999)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 772-785 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In random heteropolymer globules with short-range interactions between the monomers, freezing takes place at the microscopic length scale only, and can be described by a one-step replica symmetry breaking. The fact that the long-range Coulomb interaction has no intrinsic length scale suggests that freezing in random polyampholyte globules might take place at all length scales, corresponding to an overlap parameter q(x) that increases continuously from zero to its maximum value. Study of the polyampholyte globule within the independent interaction approximation seems to confirm this scenario. However, the independent interaction model has an important deficiency: it cannot account for self-screening, and we show that the model is only reliable at length scales shorter than the self-screening length. Using the more realistic sequence model we prove that in the general case of a random heteropolymer globule containing two types of monomers such that unlike monomers attract each other, freezing at arbitrarily large length scales is not possible. For polyampholyte globules this implies that beyond the self-screening length, the freezing behavior is qualitatively the same as in the case of short-range interactions. We find that if the polyampholyte globule is not maximally compact, the degree of frustration is insufficient to obtain freezing. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.479356
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  • 2
    Electronic Resource
    Electronic Resource
    Phase diagram analysis of random heteropolymers with composition specific and quenched cross-links (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 2947-2958 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study the conformational organization of a novel class of soft matter, random heteropolymers (RHPs) with composition specific and quenched cross-links by replica field theory. These technologically relevant materials carry an essentially quenched sequence distribution of disparate segments, and also a fixed distribution of composition specific cross-links. The chain connectivity of the linear RHPs is captured most generally by a continuous microscopic RHP Hamiltonian, while the quenched character of the cross-links is enforced by spatial constraints on segments of a prescribed composition, and by allowing fluctuations in the total number of composition specific cross-links around an experimentally controlled average. The replica theory, a formalism widely used in the study of linear RHPs, is extended in the present work to analysis of systems with multiform disorder that have interdependent disorder components. By numerically analyzing the free energy and its stability we predict the occurrence of frozen phase formation wherein few conformations are sampled. By systematically varying the sequence/cross-link fluctuations, temperature, and the RHP interaction parameters we show that two conformational transitions can occur in the frozen phase. The low temperature conformational transition resembles to a large extent the reduction in chain conformations which occurs during the folding of proteins with fixed disulfide bonds. The frozen phase domain microstructure formation is discussed in context of the recently elucidated phase diagram of a close related system, RHPs with annealed cross-links. Explicit connection is made with possible experiments and computer simulations methods to test our predictions. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476847
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  • 3
    Electronic Resource
    Electronic Resource
    Cooperativity and stability in a Langevin model of proteinlike folding (1997)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 106 (1997), S. 9276-9285 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We find that an isotropic potential energy function produces, at best, a modest degree of cooperativity. In contrast, a suitable anisotropic potential energy function delivers strong cooperativity. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.474039
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  • 4
    Electronic Resource
    Electronic Resource
    Field theory and segmental alignment analysis for a solution of sequence disordered liquid crystalline polymers (2002)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 116 (2002), S. 3134-3140 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A field theory for the many-chain mesogen/flexible sequence model is developed. The theory is solved using a creation–annihilation formalism based on a reference state that recovers the Gupta–Edwards solution for the many-chain homopolymer system. Orientational averages are performed, and a nonlinear equation for the orientational tensor-dependent free energy is derived. The effects of flexibility, stiffness and intersegment alignment on orientational ordering, the nematic/isotropic density threshold, and the segmental orientational ordering at the nematic/isotropic transition is determined. © 2002 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1430743
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  • 5
    Electronic Resource
    Electronic Resource
    Exotic phase transitions in disordered globular networks (2001)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 114 (2001), S. 10968-10976 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We present a comprehensive numerical study of phase diagram and conformational transitions in disordered globular networks with physical/chemical crosslinks. Physically crosslinked random heteropolymer (RHP) networks at positive intersegment interaction dissimilarity, i.e., χf〉0, exhibit three globular phases: frozen globular with microdomain structure, random globular, and frozen-random-globular phase, while chemically crosslinked RHPs at positive χf exhibit one random-globular phase and three frozen-globular phases; in contrast with RHPs with physical crosslinks, phase changes in chemically crosslinked RHP networks do not require reentrant passages via a random-globular phase. Based on physical grounds we explain the origins of the phase changes predicted and discuss the order of the phase transitions predicted. © 2001 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.1372760
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  • 6
    Electronic Resource
    Electronic Resource
    Enumeration of all compact conformations of copolymers with random sequence of links (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 93 (1990), S. 5967-5971 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Exhaustive enumeration of all compact self-avoiding conformations of a chain of 27 monomers on the 3*3*3 fragment of a simple cubic lattice is given. Total number of conformations unrelated by symmetry is 103 346. This number is relatively small which makes it possible to make a numerically exact calculation of all thermodynamic functions this chain. Heteropolymers with random sequence of links were considered, and the freezing transition at finite temperature was observed. This transition is analogous to folding transition in proteins where unique structure is formed. The numeric results demonstrate the equivalence between random 3-dimensional heteropolymers and the random energy model found previously in analytical investigations. The possible application of these results to some problems of combinational optimization is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.459480
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  • 7
    Electronic Resource
    Electronic Resource
    Simulation study of the collapse of linear and ring homopolymers (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 2615-2624 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The thermodynamic and kinetic properties of Lennard-Jones homopolymers are studied by computer simulation of the homopolymer at constant temperature and during collapse following an abrupt temperature drop. The homopolymer dynamics is simulated using both the Gaussian phase packet dynamics algorithm, which provides an approximate solution of the Liouville equation for the time dependent classical density distribution, and conventional molecular dynamics. Numerical simulations of both linear and ring polymers are analyzed and compared with theoretical predictions. The results support the idea that homopolymer collapse is a two-stage process. © 1995 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470522
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  • 8
    Electronic Resource
    Electronic Resource
    Conformational Entropy of a Branched Polymer (1995)
    s.l. : American Chemical Society
    Macromolecules 28 (1995), S. 3718-3727 
    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/ma00114a028
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  • 9
    Electronic Resource
    Electronic Resource
    PROTEIN FOLDING THEORY: From Lattice to All-Atom Models (2001)
    Palo Alto, Calif. : Annual Reviews
    Annual Review of Biophysics and Biomolecular Structure 30 (2001), S. 361-396 
    Details
    ISSN: 1056-8700
    Source: Annual Reviews Electronic Back Volume Collection 1932-2001ff
    Topics: Biology , Physics
    Notes: Abstract This review focuses on recent advances in understanding protein folding kinetics in the context of nucleation theory. We present basic concepts such as nucleation, folding nucleus, and transition state ensemble and then discuss recent advances and challenges in theoretical understanding of several key aspects of protein folding kinetics. We cover recent topology-based approaches as well as evolutionary studies and molecular dynamics approaches to determine protein folding nucleus and analyze other aspects of folding kinetics. Finally, we briefly discuss successful all-atom Monte-Carlo simulations of protein folding and conclude with a brief outlook for the future.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1146/annurev.biophys.30.1.361
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  • 10
    Electronic Resource
    Electronic Resource
    How does a protein fold? (1994)
    [s.l.] : Nature Publishing Group
    Nature 369 (1994), S. 248-251 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The mechanism of protein folding is not understood, despite many studies devoted to this subject1. The essential question is how a polypeptide chain is able to fold rapidly, in milliseconds to seconds, to the native state, despite the very large number of conformations that exist for the chain ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/369248a0
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