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Thomas Pfohl

Publications and source records attributed to Thomas Pfohl.

4 recordsLinked to original sources
arXiv2026

Alterations in Conformations of Poly(3-hexylthiophene) on Au(111) Induced by Annealing

Employing high-vacuum electrospray deposition and scanning tunneling microscopy, we investigated how individual poly(3-hexylthiophene) (P3HT) chains navigated on the periodic energy landscape of a reconstructed Au(111) surface. The resulting polymer conformations were governed by the interplay between the periodically corrugated substrate, in particular the depth and regularity of the modulated surface potential, and thermal energy. On a regularly reconstructed surface, annealing at {\deg}C provided sufficient energy for chain segments to overcome energy barriers of the corrugated surface potential landscape, allowing monomers along the chain to experience a strong thermodynamic driving force toward the low-energy valleys on the surface. The adsorbed polymers adopted a state where the polymer conformations were replicating the herringbone pattern. By contrast, on an irregularly reconstructed surface, the correspondingly disordered potential landscape yielded a diverse mix of coiled polymer chains performing a two-dimensional random walk and collapsed chains located in troughs of the energy landscape. Intriguingly, annealing at {\deg}C forced polymers to form clusters of many chains. Our results establish that thermal energy and substrate topography represent control parameters for altering polymer conformations, providing a mechanistic framework for rationally designing polymer nanostructures at the molecular level.

cond-mat.soft↗
arXiv2011

PAMAM6 dendrimers and DNA: pH dependent "beads-on-a-string" behavior revealed by small angle X-ray scattering

DNA interactions with polycations are not only important for our understanding of chromatin compaction but also for characterizing DNA-binding proteins involved in transcription, replication and repair. DNA is known to form several types of liquid-crystalline phases depending, among other factors, on polycation structure and charge density. Theoretical studies and simulations have predicted the wrapping of DNA around spherical positively charged polycations. As a potential mimic of the histone octamer or other DNA wrapping proteins, poly(amido amine) generation 6 (PAMAM6) dendrimers have been chosen for our study. The self-assembly of DNA induced by PAMAM6 has been investigated using small angle X-ray scattering (SAXS) in order to reveal the assemblies' structure dependence on the pH of the environment and on dendrimers concentration. We demonstrate that at pH 8.5 dense phases are formed and characterized by a 2D-columnar hexagonal lattice which is transformed into a 3D hexagonal lattice with increasing dendrimer concentration (charge ratio N/P). Moreover, a systematic analysis of the scattering data collected from diluted samples at pH 8.5 and 5.5 have led us to propose a wrapping scenario of DNA around PAMAM6 at pH 5.5.

physics.bio-ph↗
arXiv2010

Structural and dynamic properties of linker histone H1 binding to DNA

Found in all eukaryotic cells, linker histones H1 are known to bind to and rearrange nucleosomal linker DNA. In vitro, the fundamental nature of H1/DNA interactions has attracted wide interest among research communities - for biologists from a chromatin organization deciphering point of view, and for physicists from the study of polyelectrolyte interactions point of view. Hence, H1/DNA binding processes, structural and dynamical information about these self-assemblies is of broad importance. Targeting a quantitative understanding of H1 induced DNA compaction mechanisms our strategy is based on using small angle X-ray microdiffraction in combination with microfluidics. The usage of microfluidic hydrodynamic focusing devices facilitate a microscale control of these self-assembly processes. In addition, the method enables time-resolved access to structure formation in situ, in particular to transient intermediate states. The observed time dependent structure evolution shows that the interaction of H1 with DNA can be described as a two step process: an initial unspecific binding of H1 to DNA is followed by a rearrangement of molecules within the formed assemblies. The second step is most likely induced by interactions between the charged side chains of the protein and DNA. This leads to an increase in lattice spacing within the DNA/protein assembly and induces a decrease in the correlation length of the mesophases, probably due to a local bending of the DNA.

physics.bio-ph↗