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Andreas Hanke

Publications and source records attributed to Andreas Hanke.

6 recordsLinked to original sources
PubMed2004

Probing molecular free energy landscapes by periodic loading.

Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a challenge, in particular, for the unstable barrier regions. We propose a new method for obtaining the full profile by introducing a periodic ramp and using Jarzynski's relation for obtaining equilibrium quantities from nonequilibrium data. Our simulated experiments show that this method delivers significant more accurate data than previous methods, under the constraint of equal experimental effort.

Bacteriorhodopsins↗
PubMed2003

Entropy loss in long-distance DNA looping.

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow us to obtain a fast estimate for the entropy loss for a given configuration. Numerical values obtained for some examples suggest that the entropy loss encountered in loop closure in typical genetic switches may become a relevant factor in comparison to both k(B)T and typical bond energies in biopolymers, which has to be overcome by the released bond energy between the looping contact sites.

Binding Sites↗
PubMed2002

Tightness of slip-linked polymer chains.

We study the interplay between entropy and topological constraints for a polymer chain in which sliding rings (slip links) enforce pair contacts between monomers. These slip links divide a closed ring polymer into a number of subloops which can exchange length among each other. In the ideal chain limit, we find the joint probability density function for the sizes of segments within such a slip-linked polymer chain (paraknot). A particular segment is tight (small in size) or loose (of the order of the overall size of the paraknot) depending on both the number of slip links it incorporates and its competition with other segments. When self-avoiding interactions are included, scaling arguments can be used to predict the statistics of segment sizes for certain paraknot configurations.

Journal Article↗
PubMed2002

Equilibrium shapes of flat knots.

We study the equilibrium shapes of prime and composite knots confined to two dimensions. Using scaling arguments we show that, due to self-avoiding effects, the topological details of prime knots are localized on a small portion of the larger ring polymer. Within this region, the original knot configuration can assume a hierarchy of contracted shapes, the dominating one given by just one small loop. This hierarchy is investigated in detail for the flat trefoil knot, and corroborated by Monte Carlo simulations.

DNA↗
PubMed2002

Correlation functions near modulated and rough surfaces.

In a system with long-ranged correlations, the behavior of correlation functions is sensitive to the presence of a boundary. We show that surface deformations strongly modify this behavior as compared to a flat surface. The modified near surface correlations can be measured by scattering probes. To determine these correlations, we develop a perturbative calculation in the deformations in height from a flat surface. Detailed results are given for a regularly patterned surface, as well as for a self-affinely rough surface with roughness exponent zeta. By combining this perturbative calculation in height deformations with the field-theoretic renormalization-group approach, we also estimate the values of critical exponents governing the behavior of the decay of correlation functions near a self-affinely rough surface. We find that for the interacting theory, a large enough zeta can lead to a different surface critical behavior. We also provide scaling relations between roughness induced critical exponents for thermodynamic surface quantities.

Journal Article↗