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| 2. |
- Junghans, Christoph, et al.
(author)
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Thermodynamics of peptide aggregation processes: An analysis from perspectives of three statistical ensembles.
- 2008
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:8
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Journal article (peer-reviewed)abstract
- We employ a mesoscopic model for studying aggregation processes of proteinlike hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase separation process, in which the microcanonical entropy exhibits a convex intruder due to non-negligible surface effects of the small systems. We analyze thermodynamic properties of the conformational transitions accompanying the aggregation process from the multicanonical, canonical, and microcanonical perspective. It turns out that the microcanonical description is particularly advantageous as it allows for unraveling details of the phase-separation transition in the thermodynamic region, where the temperature is not a suitable external control parameter anymore.
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| 3. |
- Kallias, Anna, et al.
(author)
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Thermodynamics and kinetics of a Go(o)over-bar proteinlike heteropolymer model with two-state folding characteristics
- 2008
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In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:5, s. 7-055102
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Journal article (peer-reviewed)abstract
- We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar G (o) over bar -like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding behavior. It turns out that general, characteristic folding features of realistic proteins with a single free-energy barrier can also be observed in this simplified model, where the folding transition is primarily driven by the hydrophobic force.
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| 4. |
- Mitternacht, Simon, et al.
(author)
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Differences in solution behavior among four semiconductor-binding peptides
- 2007
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In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 111:17, s. 4355-4360
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Journal article (peer-reviewed)abstract
- Recent experiments have identified peptides that adhere to GaAs and Si surfaces. Here, we use all-atom Monte Carlo simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all with 12 residues. At room temperature, we find that all four peptides are largely unstructured, which is consistent with experimental data. At the same time, we find that one of the peptides is structurally different and more flexible, as compared to the others. This finding points at structural differences as a possible explanation for differences in adhesion properties among these peptides. By also analyzing designed mutants of two of the peptides, an experimental test of this hypothesis is proposed.
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| 5. |
- Vogel, Thomas, et al.
(author)
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Freezing and collapse of flexible polymers on regular lattices in three dimensions
- 2007
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In: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755. ; 76:6
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Journal article (peer-reviewed)abstract
- We analyze the crystallization and collapse transition of a simple model for flexible polymer chains on simple-cubic and face-centered-cubic lattices by means of sophisticated chain-growth methods. In contrast to the bond-fluctuation polymer model in certain parameter ranges, where these two conformational transitions were found to merge in the thermodynamic limit, we conclude from our results that the two transitions remain well separated in the limit of infinite chain lengths. The reason for this qualitatively distinct behavior is presumably due to the ultrashort attractive interaction range in the lattice models considered here.
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