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  • 1
    Electronic Resource
    Electronic Resource
    Folding kinetics of proteins and copolymers (1992)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 96 (1992), S. 768-780 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We model the kinetic processes by which globular proteins and other heteropolymers fold to compact states. We perform Monte Carlo dynamics simulations on short self-avoiding copolymer chains on two-dimensional square lattices. The driving force for collapse is the aversion of nonpolar monomers for water. The chain monomers are of two types, H and P; favorable interactions occur among HH contacts. One respect in which this study differs from previous Monte Carlo folding studies is that the chains are sufficiently short that: (i) we can know unequivocally which conformations are at global minima (the "native'' states) and which are at local minima of free energy, (ii) we can explore "pathway space'' densely to determine the relative probabilities of all the possible pathways, and thus we establish that the model is ergodic and gives the equilibrium distribution in the long-time limit. We find that any individual molecule passes through a wide range of conformational states, often many times. Nevertheless, this meandering is not inconsistent with the observation that proteins fold through specific pathways involving particular sequences of events. Some pathways are strongly favored; i.e., folding is "cooperative'' in that a "nucleating'' HH contact acts as a constraint that restricts local conformational freedom and speeds the "zipping up'' of other contacts nearby. Which pathways are favored depends on the sequence and the solvent. How does a chain fold to its native state so quickly? For these short chains of fixed length, we observe three regimes of folding kinetics. In the "Levinthal limit,'' as the HH attraction approaches zero, folding is slow because the molecule searches randomly through the large ensemble of open conformations. In the "multiple minima'' limit, when the HH attraction is very strong, folding is also slow because the chain becomes stuck in local minima of wrong compact conformations. However, we find that folding is relatively fast for intermediate HH attraction because the driving force "directs'' the molecule toward a small ensemble of compact states, and yet incorrect potential wells are not too deep to slow this process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.462462
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  • 2
    Electronic Resource
    Electronic Resource
    Association and fragmentation in reverse micelles (1990)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 92 (1990), S. 2036-2042 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have developed a computer simulation to model the formation of reverse micelles from the association and fragmentation of diblock polymeric chains. Using this model, we can observe the evolution of the average cluster size as a function of time. Furthermore, we can explicitly relate the aggregation number N to Ps or the breakup constant, which is inversely proportional to τ, the lifetime of the chain in the cluster. We find that Ps∼exp(−N), which differs from the scaling relationship that exists between these variables when the associating species are particles. We find that the value of τ (or Ps) affects not only the average cluster size but also, the actual mechanism of structural rearrangement for these micelles.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.458037
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  • 3
    Electronic Resource
    Electronic Resource
    The effect of polymer geometry on polymer–surfactant association in solution (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 8467-8473 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We developed a Monte Carlo computer simulation to examine the effect of polymer architecture on polymer–polymer and polymer–surfactant association in solution. Initially, we compared the self-assembly of polymers containing four associating sites with the assembling behavior of polymers containing only two such "stickers,'' one at each end of the chain. This small difference in the number of stickers lead to marked differences in the properties exhibited by the two types of chains. At short times, the two-sticker polymers form a percolating network, which fragments into small clusters at long times. The four-sticker chains do not form such a network, but form relatively large, stable clusters. Surfactant molecules were then introduced into the system and we compared the polymer–surfactant association for both polymer architectures. The surfactants effectively break up the polymer clusters for the four-sticker architecture, while they enhance the cluster size found in the two-polymer solution. The implications of this behavior on the solution viscosity are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.461276
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  • 4
    Electronic Resource
    Electronic Resource
    Contrasting the surface adsorption of comb and linear polymers (1991)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 95 (1991), S. 3798-3803 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using Monte Carlo computer simulations, we contrast the surface adsorption of comb and linear polymers that contain the same number of monomers. Both homopolymers and copolymer chains are examined. The homopolymers are composed of units that are strongly attracted to the surface ("stickers''), while the copolymers contain both stickers and sites that do not have a high affinity for the surface. Comb polymers, which contain long "sticky'' teeth, provide a higher or comparable surface coverage, thinner films, and greater polymer–surface adhesion and wettability than the equivalent linear chains. For homopolymer and copolymer combs that contain sticky teeth, the behavior of the long teeth dominate the properties of the chains at the interface. Thus differences between these two types of chains diminish as the tooth length is increased. Finally, combs that contain sticky backbones but nonsticky teeth provide a significant polymer density in the outer layers of the adsorbed film. Thus the width of the adlayer can be tailored by varying the location of the stickers in the comb polymers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.460830
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  • 5
    Electronic Resource
    Electronic Resource
    Computational studies of protein adsorption at bilayer interfaces (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 7209-7213 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We used a Monte Carlo computer simulation to determine the behavior of proteins near and within a bilayer. The bilayer is represented by a hydrophobic slab, which is bounded above and below by hydrophilic regions. The protein is modeled as a neutral, self-avoiding chain, which contains both hydrophobic and hydrophilic sites. Through these simulations, we examined the effect of sequence distribution and the strength of the interaction energies on the interfacial activity of the proteins. The findings reveal both structural and energetic conditions under which proteins will remain localized at the surface of the bilayer or, penetrate and traverse the membrane. The results provide design criteria for fabricating proteins or biopolymers that display the desired interactions with bilayers.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465437
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  • 6
    Electronic Resource
    Electronic Resource
    Copolymer adsorption onto regular surfaces (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 8244-8253 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study the transition from infinite to finite-sized loops of Gaussian chains adsorbed onto a regular patterned surface as a function of sticking energy, E, sticker concentration, C, and surface lattice constant, m. Three cases are studied in the limit of infinite chain length. In the first case, which corresponds to a finite substrate, the ratio of the maximum surface dimension to the chain length, R/N, is zero as N→∞. In the second and third cases, the number of possible sticking sites is infinite in one and two dimensions, respectively. In the first case, we find that there is a first order transition from infinite to finite loop sizes, and there exists a range of average loop size that is inaccessible. In the second and third cases no such gap exists, and the transition is continuous.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.465650
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  • 7
    Electronic Resource
    Electronic Resource
    A theoretical model for copolymer–bilayer interactions (1993)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 4168-4173 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop a theory to model the interactions between an amphiphilic copolymer and a bilayer. The copolymer is represented as a Gaussian chain, which contains an alternating arrangement of hydrophobic and hydrophilic sites along the length of the chain. The bilayer is modeled as a hydrophobic layer embedded in a hydrophilic environment. We use the transfer matrix technique to determine the polymer density profiles and the phase diagram for this system. Two distinct phases are observed. In one phase, the copolymer is localized at the surface or within the bilayer. In the second phase, the polymer is unbound or "delocalized.'' There is a continuous transition between the two phases. We also determine the scaling behavior for the density profiles. The scaling exponents agree with our analytical arguments. We discuss the implications of our findings on designing copolymers that can act as adhesives or macromolecular surfactants.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.466113
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  • 8
    Electronic Resource
    Electronic Resource
    Effects of surfactant concentration on polymer-surfactant interactions in dilute solutions: a computer model (1989)
    s.l. : American Chemical Society
    Langmuir 5 (1989), S. 1230-1234 
    Details
    ISSN: 1520-5827
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/la00089a019
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  • 9
    Electronic Resource
    Electronic Resource
    A computer model for the effect of surfactants on the aggregation of associating polymers (1989)
    s.l. : American Chemical Society
    Langmuir 5 (1989), S. 1253-1255 
    Details
    ISSN: 1520-5827
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/la00089a023
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  • 10
    Electronic Resource
    Electronic Resource
    Copolymer/copolymer blends: effect of sequence distribution on miscibility (1985)
    s.l. : American Chemical Society
    Macromolecules 18 (1985), S. 2784-2786 
    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/ma00154a076
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