Coordinators: D.W. Heermann, M. Salmhofer, U. SchwarzThursdays 14-16 o'clock
Institute for Theoretical Physics
Winter Term 2016/17 Schedule
- Thu 27.10.16 at 14 c.t.
Andreas Drews IWR, Heidelberg
The Algebraic Diagrammatic Construction: a versatile approach to excitation energies, ionization potentials and electron affinities
- Thu 17.11.16 at 14 c.t.
Michael Kastner Wallenberg Research Centre, Stellenbosch
- Thu 24.11.16 at 14 c.t.
Ulrich Keyser Cavendish Laboratory, University of Cambridge
Direct evidence for non-Markovian fluctuations of DNA threading through a solid-state nanopore
The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an accurate measurement of the velocity variation during translocation, have remained elusive. We used DNA nanotechnology to create markers along the DNA molecules . These equally spaced markers, constructed from DNA hairpins, give direct experimental access to the translocation dynamics. We analysed the translocation through conical quartz nanopores of a 7 kbp DNA double-strand labelled with six markers . On average we measure a 5% reduction in velocity during the translocation. We also find a striking correlation in velocity fluctuations with a decay constant of 100s of μs. These results shed light on hitherto unresolved problems in the dynamics of DNA translocation and provide guidance for experiments seeking to determine positional information along a DNA strand. These include localisation of bound proteins  or detection of specific sequences or in general DNA translocation dynamics in asymmetric nanochannels
- N. A. W. Bell and U. F. Keyser. Digitally encoded DNA nanostructures for multiplexed, single- molecule protein sensing with nanopores. Nature Nanotechnology, 11:645-651, 2016.
- N. A. W. Bell and U. F. Keyser. Direct Measurement reveal non-Markovian fluctuations of DNA threading through a nanopore. https://arxiv.org/abs/1607.04612
- N. A. W. Bell and U. F. Keyser. Specific Protein Detection using Designed DNA Carriers and Nanopores. JACS, 137(5):2035-2041, 2015.
- Thu 01.12.16 at 14 c.t.
Alessio Recati Arnold Sommerfeld Center for Theoretical Physics, LMU, München, Germany and INO-NR BEC Center, Trento, Italy
The repulsive branch of strongly interacting atomic Fermi gases: repulsive polaron physics and ferromagnetic instability.
The talk reviews some properties of the (metastable) repulsive branch of spin-1/2 atomic Fermi gases and it is based on the new insights coming from the recent experiments performed at the LENS in Florence [1,2].
In particular employing radio frequency spectroscopy for a polarized spin-mixture of ultracold Li-6 atoms, we investigate the properties of the so-called "repulsive polaron". We observe well-defined coherent quasiparticles even for unitarity-limited interactions and extract the key properties of repulsive Fermi polarons: the energy, the effective mass, the residue and the decay rate. Above a critical interaction, the energy is found to exceed the Fermi energy of the bath and the mass shows an instability. Such findings reveal that the paramagnetic Fermi liquid state becomes thermodynamically unstable towards an energetically favored ferromagnetic phase. However, the repulsive branch is not the ground state of the system and is affected by pairing mechanisms, which has forbidden the study of any ferromagnetic behaviour or a transition from a para- to a ferro-magnetic state within equilibrium experiments . In order to drastically reduce detrimental effects that affected previous studies, we prepare the gas in a magnetic domain-wall configuration and we study its subsequent dynamics. We observe softening of the spin-dipole collective mode, which reflects an increase of the spin susceptibility for increasing interaction strength. The dynamics changes beyond a critical interaction strength value as expected for a gas entering a ferromagnetic phase. The immiscible behaviour of the gas beyond the critical value of repulsion is additionally confirmed by the emergence of a time window during which spin diffusion vanishes. We also extract the critical values of the repulsion for the change in the dynamics as a function of the temperature. Such an approach opens up new perspectives for investigating repulsive Fermi systems.
- F. Scazza et al., arXiv:1609.09817
- G. Valtolina et al., arXiv:1605.07850
- G. Jo et al., Science 325, 1521 (2009)
- Thu 22.12.16 at 14 c.t.
Daniel Schiffels Center for Nanoscale Science and Technology National Institute of Standards & Technology
Construction of Nanoscale Devices for Quantitative, Single-Molecule Measurements of DNA-Protein Interactions
DNA origami  exploits the programmable nature of DNA base binding to create nanoscale shapes. Recently, the development of DNA origami devices such as “force clamps” has enabled quantitative measurements of protein-DNA binding interactions at the single molecule level . Construction of useful DNA based devices requires a detailed knowledge of the mechanical properties of DNA nanostructures. I will describe a systematic study of the mechanical properties of DNA nanotubes (Fig. A) including measurements of bending rigidity (persistence length), supertwist and writhe  and discuss how these properties can be tuned to create functional devices to study protein-DNA interactions. Using these well characterized DNA nanotubes, I will present a new approach towards single molecule measurements of sub-diffraction limit DNA bending deformations using a “nun-chuck” device that mechanically amplifies nano-scale DNA deformations to the micrometer-scale thus enabling a facile, real-time read-out using fluorescence microscopy . I will give an outlook as to how this type of device could be employed to study protein-induced DNA bending. I will further describe how proteins can be integrated into DNA self-assembly schemes to create complex, 3D microscale structures with addressability on the nanoscale. This can be accomplished by a hierarchical assembly process, using DNA polymerase and DNA origami folding to create a mechanically flexible skeleton, which is then rigidified by RecA protein filament assembly in precisely defined positions . These hybrid structures achieve higher folding yields, lower cost, and significantly exceed the size limitations of traditional DNA origami while offering new protein-based functionalities.
- Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297-302, (2006)
- P. C. Nickels, B. Wunsch, P. Holzmeister, W. Bae, L. M. Kneer, D. Grohmann, P. Tinnefeld, T. Liedl, Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp. Science 354, 305-307 (2016)
- D. Schiffels, T. Liedl, D. K. Fygenson, Nanoscale structure and microscale stiffness of DNA nanotubes. ACS Nano 7, 6700-6710 (2013)
- A. M. Mohammed, L. Velazquez, A. Chisenhall, D. Schiffels, D. K. Fygenson, and R. Schulman, Self-Assembly of Precisely Defined DNA Nanotube Superstructures Using DNA Origami Seeds, Nanoscale (2016)
- D. Schiffels, V. Szalai, J. Liddle, Self-Assembly of Micrometer Scale Structures with Nanometer Precision. Submitted (2016)
- Thu 12.01.17 at 14 c.t.
David Holcman Ecole Normale Superieure, Paris
Statistical methods, asymptotics and polymer models for analyzing chromatin dynamics in the cell nucleus.
The organization and dynamics of the chromatin in the cell nucleus remain unclear. Two ensembles of data are now accessible: many single particle trajectories of a DNA locus and the distribution of polymer loops across cell populations: What can be recovered about the in vivo organization of the chromatin from these data? We will present our past efforts to study loop distributions, to compute asymptotically the mean looping time in free and confined microdomains, to construct a polymer model with a prescribed anomalous exponent and to extract tethering forces from single locus trajectories. These methods are applied to study the coarse-grained geometrical organization of the chromatin from Hi-C data and to predict the dynamics of gene interactions conditioned on the statistics of the data.